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sample.vcf
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##fileformat=VCFv4.2
##FILTER=<ID=PASS,Description="All filters passed">
##fileDate=26/04/23-09:23:31
##source=FilterMutectCalls,Mutect2,lancet 1.1.0, October 18 2019
##contig=<ID=chrM,length=16571>
##contig=<ID=chr1,length=249250621>
##contig=<ID=chr2,length=243199373>
##contig=<ID=chr3,length=198022430>
##contig=<ID=chr4,length=191154276>
##contig=<ID=chr5,length=180915260>
##contig=<ID=chr6,length=171115067>
##contig=<ID=chr7,length=159138663>
##contig=<ID=chr8,length=146364022>
##contig=<ID=chr9,length=141213431>
##contig=<ID=chr10,length=135534747>
##contig=<ID=chr11,length=135006516>
##contig=<ID=chr12,length=133851895>
##contig=<ID=chr13,length=115169878>
##contig=<ID=chr14,length=107349540>
##contig=<ID=chr15,length=102531392>
##contig=<ID=chr16,length=90354753>
##contig=<ID=chr17,length=81195210>
##contig=<ID=chr18,length=78077248>
##contig=<ID=chr19,length=59128983>
##contig=<ID=chr20,length=63025520>
##contig=<ID=chr21,length=48129895>
##contig=<ID=chr22,length=51304566>
##contig=<ID=chrX,length=155270560>
##contig=<ID=chrY,length=59373566>
##contig=<ID=chr1_gl000191_random,length=106433>
##contig=<ID=chr1_gl000192_random,length=547496>
##contig=<ID=chr4_ctg9_hap1,length=590426>
##contig=<ID=chr4_gl000193_random,length=189789>
##contig=<ID=chr4_gl000194_random,length=191469>
##contig=<ID=chr6_apd_hap1,length=4622290>
##contig=<ID=chr6_cox_hap2,length=4795371>
##contig=<ID=chr6_dbb_hap3,length=4610396>
##contig=<ID=chr6_mann_hap4,length=4683263>
##contig=<ID=chr6_mcf_hap5,length=4833398>
##contig=<ID=chr6_qbl_hap6,length=4611984>
##contig=<ID=chr6_ssto_hap7,length=4928567>
##contig=<ID=chr7_gl000195_random,length=182896>
##contig=<ID=chr8_gl000196_random,length=38914>
##contig=<ID=chr8_gl000197_random,length=37175>
##contig=<ID=chr9_gl000198_random,length=90085>
##contig=<ID=chr9_gl000199_random,length=169874>
##contig=<ID=chr9_gl000200_random,length=187035>
##contig=<ID=chr9_gl000201_random,length=36148>
##contig=<ID=chr11_gl000202_random,length=40103>
##contig=<ID=chr17_ctg5_hap1,length=1680828>
##contig=<ID=chr17_gl000203_random,length=37498>
##contig=<ID=chr17_gl000204_random,length=81310>
##contig=<ID=chr17_gl000205_random,length=174588>
##contig=<ID=chr17_gl000206_random,length=41001>
##contig=<ID=chr18_gl000207_random,length=4262>
##contig=<ID=chr19_gl000208_random,length=92689>
##contig=<ID=chr19_gl000209_random,length=159169>
##contig=<ID=chr21_gl000210_random,length=27682>
##contig=<ID=chrUn_gl000211,length=166566>
##contig=<ID=chrUn_gl000212,length=186858>
##contig=<ID=chrUn_gl000213,length=164239>
##contig=<ID=chrUn_gl000214,length=137718>
##contig=<ID=chrUn_gl000215,length=172545>
##contig=<ID=chrUn_gl000216,length=172294>
##contig=<ID=chrUn_gl000217,length=172149>
##contig=<ID=chrUn_gl000218,length=161147>
##contig=<ID=chrUn_gl000219,length=179198>
##contig=<ID=chrUn_gl000220,length=161802>
##contig=<ID=chrUn_gl000221,length=155397>
##contig=<ID=chrUn_gl000222,length=186861>
##contig=<ID=chrUn_gl000223,length=180455>
##contig=<ID=chrUn_gl000224,length=179693>
##contig=<ID=chrUn_gl000225,length=211173>
##contig=<ID=chrUn_gl000226,length=15008>
##contig=<ID=chrUn_gl000227,length=128374>
##contig=<ID=chrUn_gl000228,length=129120>
##contig=<ID=chrUn_gl000229,length=19913>
##contig=<ID=chrUn_gl000230,length=43691>
##contig=<ID=chrUn_gl000231,length=27386>
##contig=<ID=chrUn_gl000232,length=40652>
##contig=<ID=chrUn_gl000233,length=45941>
##contig=<ID=chrUn_gl000234,length=40531>
##contig=<ID=chrUn_gl000235,length=34474>
##contig=<ID=chrUn_gl000236,length=41934>
##contig=<ID=chrUn_gl000237,length=45867>
##contig=<ID=chrUn_gl000238,length=39939>
##contig=<ID=chrUn_gl000239,length=33824>
##contig=<ID=chrUn_gl000240,length=41933>
##contig=<ID=chrUn_gl000241,length=42152>
##contig=<ID=chrUn_gl000242,length=43523>
##contig=<ID=chrUn_gl000243,length=43341>
##contig=<ID=chrUn_gl000244,length=39929>
##contig=<ID=chrUn_gl000245,length=36651>
##contig=<ID=chrUn_gl000246,length=38154>
##contig=<ID=chrUn_gl000247,length=36422>
##contig=<ID=chrUn_gl000248,length=39786>
##contig=<ID=chrUn_gl000249,length=38502>
##FILTER=<ID=FAIL,Description="Fail the site if all alleles fail but for different reasons.">
##FILTER=<ID=base_qual,Description="alt median base quality">
##FILTER=<ID=clustered_events,Description="Clustered events observed in the tumor">
##FILTER=<ID=contamination,Description="contamination">
##FILTER=<ID=duplicate,Description="evidence for alt allele is overrepresented by apparent duplicates">
##FILTER=<ID=fragment,Description="abs(ref - alt) median fragment length">
##FILTER=<ID=germline,Description="Evidence indicates this site is germline, not somatic">
##FILTER=<ID=haplotype,Description="Variant near filtered variant on same haplotype.">
##FILTER=<ID=low_allele_frac,Description="Allele fraction is below specified threshold">
##FILTER=<ID=map_qual,Description="ref - alt median mapping quality">
##FILTER=<ID=multiallelic,Description="Site filtered because too many alt alleles pass tumor LOD">
##FILTER=<ID=n_ratio,Description="Ratio of N to alt exceeds specified ratio">
##FILTER=<ID=normal_artifact,Description="artifact_in_normal">
##FILTER=<ID=orientation,Description="orientation bias detected by the orientation bias mixture model">
##FILTER=<ID=panel_of_normals,Description="Blacklisted site in panel of normals">
##FILTER=<ID=position,Description="median distance of alt variants from end of reads">
##FILTER=<ID=possible_numt,Description="Allele depth is below expected coverage of NuMT in autosome">
##FILTER=<ID=slippage,Description="Site filtered due to contraction of short tandem repeat region">
##FILTER=<ID=strand_bias,Description="Evidence for alt allele comes from one read direction only">
##FILTER=<ID=strict_strand,Description="Evidence for alt allele is not represented in both directions">
##FILTER=<ID=weak_evidence,Description="Mutation does not meet likelihood threshold">
##FILTER=<ID=LowCovNormal,Description="Low coverage in the normal (<10)">
##FILTER=<ID=HighCovNormal,Description="High coverage in the normal (>1000000)">
##FILTER=<ID=LowCovTumor,Description="Low coverage in the tumor (<4)">
##FILTER=<ID=HighCovTumor,Description="High coverage in the tumor (>1000000)">
##FILTER=<ID=LowVafTumor,Description="Low variant allele frequency in the tumor (<0.04)">
##FILTER=<ID=HighVafNormal,Description="High variant allele frequency in the normal (>0)">
##FILTER=<ID=LowAltCntTumor,Description="Low alternative allele count in the tumor (<3)">
##FILTER=<ID=HighAltCntNormal,Description="High alternative allele count in the normal (>0)">
##FILTER=<ID=LowFisherScore,Description="Low Fisher's exact test score for tumor-normal allele counts (<5)">
##FILTER=<ID=LowFisherSTR,Description="Low Fisher's exact test score for tumor-normal STR allele counts (<25)">
##FILTER=<ID=StrandBias,Description="Strand bias: # of non-reference reads in either forward or reverse strand below threshold (<1)">
##FILTER=<ID=STR,Description="Microsatellite mutation">
##INFO=<ID=SOURCES,Number=1,Type=String,Description="SNV callers (mutect2,lancet)">
##INFO=<ID=AS_FilterStatus,Number=A,Type=String,Description="Filter status for each allele, as assessed by ApplyVQSR. Note that the VCF filter field will reflect the most lenient/sensitive status across all alleles.">
##INFO=<ID=AS_SB_TABLE,Number=1,Type=String,Description="Allele-specific forward/reverse read counts for strand bias tests. Includes the reference and alleles separated by |.">
##INFO=<ID=AS_UNIQ_ALT_READ_COUNT,Number=A,Type=Integer,Description="Number of reads with unique start and mate end positions for each alt at a variant site">
##INFO=<ID=CONTQ,Number=1,Type=Float,Description="Phred-scaled qualities that alt allele are not due to contamination">
##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered">
##INFO=<ID=ECNT,Number=1,Type=Integer,Description="Number of events in this haplotype">
##INFO=<ID=GERMQ,Number=1,Type=Integer,Description="Phred-scaled quality that alt alleles are not germline variants">
##INFO=<ID=MBQ,Number=R,Type=Integer,Description="median base quality by allele">
##INFO=<ID=MFRL,Number=R,Type=Integer,Description="median fragment length by allele">
##INFO=<ID=MMQ,Number=R,Type=Integer,Description="median mapping quality by allele">
##INFO=<ID=MPOS,Number=A,Type=Integer,Description="median distance from end of read">
##INFO=<ID=NALOD,Number=A,Type=Float,Description="Negative log 10 odds of artifact in normal with same allele fraction as tumor">
##INFO=<ID=NCount,Number=1,Type=Integer,Description="Count of N bases in the pileup">
##INFO=<ID=NLOD,Number=A,Type=Float,Description="Normal log 10 likelihood ratio of diploid het or hom alt genotypes">
##INFO=<ID=OCM,Number=1,Type=Integer,Description="Number of alt reads whose original alignment doesn't match the current contig.">
##INFO=<ID=PON,Number=0,Type=Flag,Description="site found in panel of normals">
##INFO=<ID=POPAF,Number=A,Type=Float,Description="negative log 10 population allele frequencies of alt alleles">
##INFO=<ID=ROQ,Number=1,Type=Float,Description="Phred-scaled qualities that alt allele are not due to read orientation artifact">
##INFO=<ID=RPA,Number=R,Type=Integer,Description="Number of times tandem repeat unit is repeated, for each allele (including reference)">
##INFO=<ID=RU,Number=1,Type=String,Description="Tandem repeat unit (bases)">
##INFO=<ID=SEQQ,Number=1,Type=Integer,Description="Phred-scaled quality that alt alleles are not sequencing errors">
##INFO=<ID=STR,Number=0,Type=Flag,Description="Variant is a short tandem repeat">
##INFO=<ID=STRANDQ,Number=1,Type=Integer,Description="Phred-scaled quality of strand bias artifact">
##INFO=<ID=STRQ,Number=1,Type=Integer,Description="Phred-scaled quality that alt alleles in STRs are not polymerase slippage errors">
##INFO=<ID=TLOD,Number=A,Type=Float,Description="Log 10 likelihood ratio score of variant existing versus not existing">
##INFO=<ID=FETS,Number=1,Type=Float,Description="Phred-scaled p-value of the Fisher's exact test for tumor-normal allele counts">
##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description="Somatic mutation">
##INFO=<ID=SHARED,Number=0,Type=Flag,Description="Shared mutation betweem tumor and normal">
##INFO=<ID=NORMAL,Number=0,Type=Flag,Description="Mutation present only in the normal">
##INFO=<ID=NONE,Number=0,Type=Flag,Description="Mutation not supported by data">
##INFO=<ID=KMERSIZE,Number=1,Type=Integer,Description="K-mer size used to assemble the locus">
##INFO=<ID=SB,Number=1,Type=Float,Description="Strand bias score: phred-scaled p-value of the Fisher's exact test for the forward/reverse read counts in the tumor">
##INFO=<ID=MS,Number=1,Type=String,Description="Microsatellite mutation (format: #LEN#MOTIF)">
##INFO=<ID=LEN,Number=1,Type=Integer,Description="Variant size in base pairs">
##INFO=<ID=TYPE,Number=1,Type=String,Description="Variant type (snv, del, ins, complex)">
##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
##FORMAT=<ID=AF,Number=A,Type=Float,Description="Allele fractions of alternate alleles in the tumor">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">
##FORMAT=<ID=F1R2,Number=R,Type=Integer,Description="Count of reads in F1R2 pair orientation supporting each allele">
##FORMAT=<ID=F2R1,Number=R,Type=Integer,Description="Count of reads in F2R1 pair orientation supporting each allele">
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=PGT,Number=1,Type=String,Description="Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another; will always be heterozygous and is not intended to describe called alleles">
##FORMAT=<ID=PID,Number=1,Type=String,Description="Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group">
##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">
##FORMAT=<ID=PS,Number=1,Type=Integer,Description="Phasing set (typically the position of the first variant in the set)">
##FORMAT=<ID=SB,Number=4,Type=Integer,Description="Per-sample component statistics which comprise the Fisher's Exact Test to detect strand bias.">
##FORMAT=<ID=SR,Number=.,Type=Integer,Description="Strand counts for ref: # of supporting forward,reverse reads for reference allele">
##FORMAT=<ID=SA,Number=.,Type=Integer,Description="Strand counts for alt: # of supporting forward,reverse reads for alterantive allele">
##reference=file:///ref_dir/ucsc.hg19.fasta
##INFO=<ID=IMPRECISE,Number=0,Type=Flag,Description="Imprecise structural variation">
##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">
##INFO=<ID=SVLEN,Number=.,Type=Integer,Description="Difference in length between REF and ALT alleles">
##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the variant described in this record">
##INFO=<ID=CIPOS,Number=2,Type=Integer,Description="Confidence interval around POS">
##INFO=<ID=CIEND,Number=2,Type=Integer,Description="Confidence interval around END">
##INFO=<ID=CIGAR,Number=A,Type=String,Description="CIGAR alignment for each alternate indel allele">
##INFO=<ID=MATEID,Number=.,Type=String,Description="ID of mate breakend">
##INFO=<ID=EVENT,Number=1,Type=String,Description="ID of event associated to breakend">
##INFO=<ID=HOMLEN,Number=.,Type=Integer,Description="Length of base pair identical homology at event breakpoints">
##INFO=<ID=HOMSEQ,Number=.,Type=String,Description="Sequence of base pair identical homology at event breakpoints">
##INFO=<ID=SVINSLEN,Number=.,Type=Integer,Description="Length of insertion">
##INFO=<ID=SVINSSEQ,Number=.,Type=String,Description="Sequence of insertion">
##INFO=<ID=LEFT_SVINSSEQ,Number=.,Type=String,Description="Known left side of insertion for an insertion of unknown length">
##INFO=<ID=RIGHT_SVINSSEQ,Number=.,Type=String,Description="Known right side of insertion for an insertion of unknown length">
##INFO=<ID=PAIR_COUNT,Number=1,Type=Integer,Description="Read pairs supporting this variant where both reads are confidently mapped">
##INFO=<ID=BND_PAIR_COUNT,Number=1,Type=Integer,Description="Confidently mapped reads supporting this variant at this breakend (mapping may not be confident at remote breakend)">
##INFO=<ID=UPSTREAM_PAIR_COUNT,Number=1,Type=Integer,Description="Confidently mapped reads supporting this variant at the upstream breakend (mapping may not be confident at downstream breakend)">
##INFO=<ID=DOWNSTREAM_PAIR_COUNT,Number=1,Type=Integer,Description="Confidently mapped reads supporting this variant at this downstream breakend (mapping may not be confident at upstream breakend)">
##ALT=<ID=DEL,Description="Deletion">
##ALT=<ID=INS,Description="Insertion">
##ALT=<ID=DUP:TANDEM,Description="Tandem Duplication">
##cmdline=manta-1.6.0.centos6_x86_64/bin/configManta.py --tumorBam /bam_dir/OncoSpan.rmdup.bam --referenceFasta /ref_dir/ucsc.hg19.fasta --exome --runDir /vcf_dir/
##bcftools_mergeVersion=1.13+htslib-1.13+ds
##bcftools_mergeCommand=merge --force-samples /home/gencardio/Desktop/NGS_APP/data/RUN20230425-CGC64004/GenOncology-Dx/OncoSpan/VCF_FOLDER/OncoSpan.mutect2.lancet.vcf.gz /home/gencardio/Desktop/NGS_APP/data/RUN20230425-CGC64004/GenOncology-Dx/OncoSpan/VCF_FOLDER/results/variants/candidateSV.vcf.gz; Date=Wed Apr 26 09:32:03 2023
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT OncoSpan
chr1 65310268 MantaDEL:11:0:0:0:1:0 GAAGGCAGGAGATC G . . END=65310281;SVTYPE=DEL;SVLEN=-13;CIPOS=0,3;HOMLEN=3;HOMSEQ=AAG;UPSTREAM_PAIR_COUNT=0;DOWNSTREAM_PAIR_COUNT=0;PAIR_COUNT=0;CIGAR=1M13D . .
chr1 65310489 . T C . PASS AS_SB_TABLE=367,406|252,253;ECNT=1;GERMQ=69;SOURCES=mutect2;DP=1348;AS_FilterStatus=SITE;MBQ=38,38;MFRL=158,150;MMQ=60,60;MPOS=18;POPAF=0.452;TLOD=1597.3 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:773,505:0.393:1278:361,233:306,193:367,406,252,253
chr1 65312342 . G A . PASS AS_SB_TABLE=550,263|281,123;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=1273;AS_FilterStatus=SITE;MBQ=38,38;MFRL=154,155;MMQ=60,60;MPOS=19;POPAF=1.31;TLOD=1243.07 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:813,404:0.332:1217:377,197:333,145:550,263,281,123
chr1 65321388 . G A . PASS AS_SB_TABLE=89,394|37,237;ECNT=1;GERMQ=75;SOURCES=mutect2;DP=780;AS_FilterStatus=SITE;MBQ=38,38;MFRL=175,186;MMQ=60,60;MPOS=20;POPAF=0.405;TLOD=895.2 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:483,274:0.37:757:246,148:175,102:89,394,37,237
chr1 65325970 . C T . PASS AS_SB_TABLE=41,457|18,285;ECNT=1;GERMQ=51;SOURCES=mutect2;DP=832;AS_FilterStatus=SITE;MBQ=38,38;MFRL=183,191;MMQ=60,60;MPOS=19;POPAF=0.402;TLOD=1011.95 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:498,303:0.382:801:283,170:177,112:41,457,18,285
chr1 65326098 MantaDEL:14:0:0:0:2:0 CATGCATTTATTTATTT C . . END=65326114;SVTYPE=DEL;SVLEN=-16;CIPOS=0,2;HOMLEN=2;HOMSEQ=AT;UPSTREAM_PAIR_COUNT=0;DOWNSTREAM_PAIR_COUNT=0;PAIR_COUNT=0;CIGAR=1M16D . .
chr1 65330682 . G A . germline AS_SB_TABLE=15,248|13,162;ECNT=1;GERMQ=1;SOURCES=mutect2;DP=474;AS_FilterStatus=SITE;MBQ=38,38;MFRL=239,246;MMQ=60,60;MPOS=22;POPAF=0.47;TLOD=603.2 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:263,175:0.398:438:135,97:122,76:15,248,13,162
chr1 65332696 . G A . PASS AS_SB_TABLE=567,530|56,48;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=1310;AS_FilterStatus=SITE;MBQ=38,38;MFRL=201,202;MMQ=60,60;MPOS=18;POPAF=7.3;TLOD=270.2 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:1097,104:0.088:1201:579,46:449,53:567,530,56,48
chr1 115256530 . G T . PASS AS_SB_TABLE=337,647|49,96;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=1223;AS_FilterStatus=SITE;MBQ=38,38;MFRL=160,172;MMQ=60,60;MPOS=18;POPAF=7.3;TLOD=394.84 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:984,145:0.132:1129:496,65:354,67:337,647,49,96
chr1 156785356 . T C 0 LowFisherScore;StrandBias SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=13;SB=0;SOURCES=lancet GT:AD:SR:SA:DP 1/1:0,183:0,0:183,0:183
chr1 156785544 . AC A 0.332231 LowFisherScore SOMATIC;FETS=0.332231;TYPE=del;LEN=1;KMERSIZE=13;SB=14.5611;SOURCES=lancet GT:AD:SR:SA:DP 0/1:1282,102:756,526:67,35:1384
chr1 156785617 . G A 0 LowFisherScore SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=13;SB=2.85217;SOURCES=mutect2,lancet GT:AD:SR:SA:DP 0/1:1,1698:0,1:818,880:1699
chr1 156785762 . AG A 0 LowFisherScore;HighVafNormal;HighAltCntNormal SHARED;FETS=0;TYPE=del;LEN=1;KMERSIZE=13;SB=0;SOURCES=lancet GT:AD:SR:SA:DP 1/1:0,482:0,0:48,434:482
chr1 156785771 . A G 0 LowFisherScore;HighVafNormal;HighAltCntNormal SHARED;FETS=0;TYPE=snv;LEN=1;KMERSIZE=13;SB=0;SOURCES=mutect2,lancet GT:AD:SR:SA:DP 1/1:0,532:0,0:57,475:532
chr1 156785774 . C A 0 LowFisherScore SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=15;SB=0;SOURCES=mutect2,lancet GT:AD:SR:SA:DP 1/1:0,31:0,0:1,30:31
chr1 156785779 . G A 0 LowFisherScore;HighVafNormal;HighAltCntNormal SHARED;FETS=0;TYPE=snv;LEN=1;KMERSIZE=13;SB=0;SOURCES=mutect2,lancet GT:AD:SR:SA:DP 1/1:0,476:0,0:40,436:476
chr1 156836838 . T C . PASS AS_SB_TABLE=222,740|28,58;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=1077;AS_FilterStatus=SITE;MBQ=38,37;MFRL=165,159;MMQ=60,60;MPOS=16;POPAF=0.907;TLOD=197.81 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:962,86:0.078:1048:479,46:358,25:222,740,28,58
chr1 156837847 . T C . PASS AS_SB_TABLE=148,8|10,0;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=188;AS_FilterStatus=SITE;MBQ=38,38;MFRL=207,240;MMQ=60,60;MPOS=18;POPAF=1.37;TLOD=24.59 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:156,10:0.068:166:62,3:84,7:148,8,10,0
chr1 156843543 . T C . PASS AS_SB_TABLE=637,166|39,17;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=880;AS_FilterStatus=SITE;MBQ=38,38;MFRL=169,172;MMQ=60,60;MPOS=18;POPAF=7.3;TLOD=133.44 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:803,56:0.065:859:386,26:354,24:637,166,39,17
chr1 156846233 . G A 0 LowFisherScore SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=15;SB=14.9169;SOURCES=mutect2,lancet GT:AD:SR:SA:DP 0/1:651,720:387,264:413,307:1371
chr1 156846307 . GC G 1.43917 LowFisherScore SOMATIC;FETS=1.43917;TYPE=del;LEN=1;KMERSIZE=15;SB=14.1701;SOURCES=lancet GT:AD:SR:SA:DP 0/1:1096,431:391,705:146,285:1527
chr1 156846426 . C A 0 LowFisherScore;LowVafTumor;LowAltCntTumor;StrandBias SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=21;SB=0.356395;SOURCES=lancet GT:AD:SR:SA:DP 0/1:297,2:12,285:0,2:299
chr1 156848995 . C T . germline AS_SB_TABLE=519,352|512,279;ECNT=1;GERMQ=1;SOURCES=mutect2;DP=1765;AS_FilterStatus=SITE;MBQ=38,38;MFRL=166,169;MMQ=60,60;MPOS=19;POPAF=0.245;TLOD=2646.89 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:871,791:0.476:1662:406,383:359,322:519,352,512,279
chr1 156849827 . C T . PASS AS_SB_TABLE=765,471|4,8;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=1292;AS_FilterStatus=SITE;MBQ=38,29;MFRL=156,116;MMQ=60,60;MPOS=19;POPAF=7.3;TLOD=15.58 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:1236,12:0.009085:1248:579,3:465,6:765,471,4,8
chr1 162722846 . C G . germline AS_SB_TABLE=0,0|595,167;ECNT=1;GERMQ=1;SOURCES=mutect2;DP=794;AS_FilterStatus=SITE;MBQ=0,38;MFRL=0,190;MMQ=60,60;MPOS=22;POPAF=0.009217;TLOD=3050.56 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:0,762:0.999:762:0,398:0,314:0,0,595,167
chr1 162723066 MantaBND:29:0:1:0:1:0:1 C C[chr2:70335208[ . . SVTYPE=BND;MATEID=MantaBND:29:0:1:0:1:0:0;CIPOS=0,4;HOMLEN=4;HOMSEQ=TGGG;BND_PAIR_COUNT=1;PAIR_COUNT=1 . .
chr1 162724579 . G A . PASS AS_SB_TABLE=701,659|64,74;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=1533;AS_FilterStatus=SITE;MBQ=38,38;MFRL=172,187;MMQ=60,60;MPOS=19;POPAF=7.3;TLOD=366.09 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:1360,138:0.096:1498:684,66:554,63:701,659,64,74
chr1 162725655 . A C . germline AS_SB_TABLE=0,0|0,333;ECNT=1;GERMQ=1;SOURCES=mutect2;DP=350;AS_FilterStatus=SITE;MBQ=0,38;MFRL=0,265;MMQ=60,60;MPOS=18;POPAF=0.022;TLOD=1380.79 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:0,333:0.997:333:0,197:0,133:0,0,0,333
chr1 162737116 . C G . PASS AS_SB_TABLE=193,484|68,200;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=1026;AS_FilterStatus=SITE;MBQ=38,38;MFRL=167,169;MMQ=60,60;MPOS=19;POPAF=0.636;TLOD=848.86 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:677,268:0.288:945:338,137:263,105:193,484,68,200
chr1 162740327 . T C . germline AS_SB_TABLE=0,0|72,705;ECNT=1;GERMQ=1;SOURCES=mutect2;DP=800;AS_FilterStatus=SITE;MBQ=0,38;MFRL=0,204;MMQ=60,60;MPOS=22;POPAF=0.017;TLOD=3143.51 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:0,777:0.999:777:0,434:0,287:0,0,72,705
chr1 162743418 . G T . germline AS_SB_TABLE=0,0|64,662;ECNT=1;GERMQ=1;SOURCES=mutect2;DP=759;AS_FilterStatus=SITE;MBQ=0,38;MFRL=0,205;MMQ=60,60;MPOS=15;POPAF=0.001305;TLOD=2981.45 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:0,726:0.999:726:0,384:0,288:0,0,64,662
chr1 162749761 . T C 0 LowFisherScore;StrandBias SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=21;SB=0;SOURCES=lancet GT:AD:SR:SA:DP 1/1:0,106:0,0:106,0:106
chr1 162749810 . A T 0 LowFisherScore;LowVafTumor;LowAltCntTumor;StrandBias SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=21;SB=0;SOURCES=lancet GT:AD:SR:SA:DP 0/1:159,2:159,0:2,0:161
chr1 162749851 . A T 0 LowFisherScore;LowVafTumor;LowAltCntTumor;StrandBias SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=21;SB=0;SOURCES=lancet GT:AD:SR:SA:DP 0/1:234,2:234,0:2,0:236
chr1 162750208 . C T 0 LowFisherScore SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=17;SB=0;SOURCES=lancet GT:AD:SR:SA:DP 1/1:0,13:0,0:2,11:13
chr1 243668597 . C T . PASS AS_SB_TABLE=350,430|164,146;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=1141;AS_FilterStatus=SITE;MBQ=38,38;MFRL=170,176;MMQ=60,60;MPOS=19;POPAF=7.3;TLOD=939.14 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:780,310:0.282:1090:410,165:289,114:350,430,164,146
chr1 243675511 . C T . PASS AS_SB_TABLE=52,0|3,0;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=63;AS_FilterStatus=SITE;MBQ=38,38;MFRL=291,335;MMQ=60,60;MPOS=18;POPAF=7.3;TLOD=6.64 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:52,3:0.069:55:35,3:16,0:52,0,3,0
chr1 243736039 . C T 0 LowFisherScore;StrandBias SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=15;SB=0;SOURCES=lancet GT:AD:SR:SA:DP 0/1:53,7:53,0:7,0:60
chr1 243736135 . T C 0 LowFisherScore;LowVafTumor;LowAltCntTumor;StrandBias SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=17;SB=0;SOURCES=lancet GT:AD:SR:SA:DP 0/1:194,2:194,0:2,0:196
chr1 243736141 . CA C 0 LowFisherScore;StrandBias SOMATIC;FETS=0;TYPE=del;LEN=1;KMERSIZE=17;SB=0;SOURCES=lancet GT:AD:SR:SA:DP 0/1:235,21:235,0:21,0:256
chr1 243736190 . G A 0 LowFisherScore;LowVafTumor;LowAltCntTumor;StrandBias SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=17;SB=0.114857;SOURCES=lancet GT:AD:SR:SA:DP 0/1:303,2:299,4:2,0:305
chr1 243736203 . T C 0 LowFisherScore;LowVafTumor;LowAltCntTumor;StrandBias SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=17;SB=0.336398;SOURCES=lancet GT:AD:SR:SA:DP 0/1:446,2:429,17:2,0:448
chr1 243736217 . T C 0 LowFisherSTR;LowVafTumor;LowAltCntTumor;StrandBias SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=17;SB=0.843044;MS=8T;SOURCES GT:AD:SR:SA:DP 0/1:485,2:440,45:2,0:487
chr1 243736218 . T C 0 LowFisherSTR;LowVafTumor;LowAltCntTumor;StrandBias SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=17;SB=0.894516;MS=7T;SOURCES GT:AD:SR:SA:DP 0/1:489,2:441,48:2,0:491
chr1 243736307 . C T 0.0170201 LowFisherScore;LowVafTumor SOMATIC;FETS=0.0170201;TYPE=snv;LEN=1;KMERSIZE=17;SB=4.44742;SOURCES=lancet GT:AD:SR:SA:DP 0/1:763,3:398,365:1,2:766
chr1 243776952 . T C . PASS AS_SB_TABLE=113,99|7,2;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=243;AS_FilterStatus=SITE;MBQ=38,38;MFRL=157,155;MMQ=60,60;MPOS=14;POPAF=7.3;TLOD=18.32 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:212,9:0.045:221:116,3:65,5:113,99,7,2
chr1 243777066 . G A . germline AS_SB_TABLE=0,4|0,121;ECNT=1;GERMQ=1;SOURCES=mutect2;DP=131;AS_FilterStatus=SITE;MBQ=38,38;MFRL=219,207;MMQ=60,60;MPOS=12;POPAF=0.672;TLOD=491.8 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:4,121:0.961:125:2,63:2,55:0,4,0,121
chr1 243828126 . G T . PASS AS_SB_TABLE=82,125|1,3;ECNT=2;GERMQ=93;SOURCES=mutect2;DP=218;AS_FilterStatus=SITE;MBQ=38,38;MFRL=150,167;MMQ=60,60;MPOS=31;POPAF=7.3;TLOD=6.98 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:207,4:0.026:211:124,4:62,0:82,125,1,3
chr1 243828180 . G C . PASS AS_SB_TABLE=24,171|0,7;ECNT=2;GERMQ=93;SOURCES=mutect2;DP=219;AS_FilterStatus=SITE;MBQ=38,38;MFRL=183,210;MMQ=60,60;MPOS=7;POPAF=7.3;TLOD=14.76 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:195,7:0.04:202:83,6:58,0:24,171,0,7
chr1 244006564 . A G . PASS AS_SB_TABLE=82,571|0,18;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=729;AS_FilterStatus=SITE;MBQ=38,38;MFRL=189,223;MMQ=60,60;MPOS=8;POPAF=7.3;TLOD=36.19 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:653,18:0.028:671:326,11:257,6:82,571,0,18
chr2 29416326 . G A . clustered_events AS_SB_TABLE=491,586|185,234;ECNT=3;GERMQ=93;SOURCES=mutect2;DP=1558;AS_FilterStatus=SITE;MBQ=38,38;MFRL=178,180;MMQ=60,60;MPOS=17;POPAF=7.3;TLOD=1291.79 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:1077,419:0.282:1496:512,204:453,165:491,586,185,234
chr2 29416357 . G A . clustered_events AS_SB_TABLE=591,637|40,47;ECNT=3;GERMQ=93;SOURCES=mutect2;DP=1354;AS_FilterStatus=SITE;MBQ=38,38;MFRL=185,186;MMQ=60,60;MPOS=17;POPAF=1.85;TLOD=215.94 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:1228,87:0.066:1315:553,36:466,34:591,637,40,47
chr2 29416366 . G C . clustered_events AS_SB_TABLE=360,385|275,284;ECNT=3;GERMQ=3;SOURCES=mutect2;DP=1435;AS_FilterStatus=SITE;MBQ=38,38;MFRL=188,188;MMQ=60,60;MPOS=15;POPAF=0.331;TLOD=1870.4 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:745,559:0.429:1304:325,253:277,188:360,385,275,284
chr2 29416481 . T C . PASS AS_SB_TABLE=660,569|76,72;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=1505;AS_FilterStatus=SITE;MBQ=38,38;MFRL=186,178;MMQ=60,60;MPOS=19;POPAF=0.569;TLOD=367.23 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:1229,148:0.104:1377:615,69:529,62:660,569,76,72
chr2 29416572 . T C . germline AS_SB_TABLE=0,0|758,749;ECNT=2;GERMQ=1;SOURCES=mutect2;DP=1584;AS_FilterStatus=SITE;MBQ=0,38;MFRL=0,174;MMQ=60,60;MPOS=18;POPAF=0.003488;TLOD=5891.98 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:0,1507:0.999:1507:0,776:0,575:0,0,758,749
chr2 29416615 . G A . PASS AS_SB_TABLE=479,600|188,279;ECNT=2;GERMQ=93;SOURCES=mutect2;DP=1597;AS_FilterStatus=SITE;MBQ=38,38;MFRL=178,173;MMQ=60,60;MPOS=17;POPAF=0.939;TLOD=1457.28 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:1079,467:0.306:1546:463,195:362,156:479,600,188,279
chr2 29416794 . G A . PASS AS_SB_TABLE=105,436|43,182;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=818;AS_FilterStatus=SITE;MBQ=38,38;MFRL=190,198;MMQ=60,60;MPOS=20;POPAF=0.706;TLOD=726.98 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:541,225:0.297:766:282,132:205,73:105,436,43,182
chr2 29419591 . G T . germline AS_SB_TABLE=274,24|307,24;ECNT=1;GERMQ=1;SOURCES=mutect2;DP=634;AS_FilterStatus=SITE;MBQ=38,38;MFRL=185,198;MMQ=60,60;MPOS=21;POPAF=0.286;TLOD=1168.09 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:298,331:0.53:629:158,189:127,134:274,24,307,24
chr2 29420501 . T C . PASS AS_SB_TABLE=277,461|17,36;ECNT=2;GERMQ=93;SOURCES=mutect2;DP=836;AS_FilterStatus=SITE;MBQ=38,38;MFRL=158,171;MMQ=60,60;MPOS=19;POPAF=7.3;TLOD=131.11 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:738,53:0.07:791:339,26:291,20:277,461,17,36
chr2 29420544 . T C . PASS AS_SB_TABLE=133,511|1,22;ECNT=2;GERMQ=93;SOURCES=mutect2;DP=724;AS_FilterStatus=SITE;MBQ=38,38;MFRL=164,179;MMQ=60,60;MPOS=21;POPAF=7.3;TLOD=52.48 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:644,23:0.039:667:246,6:181,7:133,511,1,22
chr2 29430519 . G T 0 LowFisherScore SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=19;SB=6.73828;SOURCES=lancet GT:AD:SR:SA:DP 0/1:28,7:25,3:5,2:35
chr2 29445458 . G T . PASS AS_SB_TABLE=785,888|80,110;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=2020;AS_FilterStatus=SITE;MBQ=38,38;MFRL=184,183;MMQ=60,60;MPOS=17;POPAF=0.569;TLOD=481.57 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:1673,190:0.1:1863:853,98:657,66:785,888,80,110
chr2 29445798 . T C . germline AS_SB_TABLE=3,1|1007,1047;ECNT=1;GERMQ=1;SOURCES=mutect2;DP=2139;AS_FilterStatus=SITE;MBQ=34,38;MFRL=130,187;MMQ=60,60;MPOS=19;POPAF=0.023;TLOD=8043.45 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:4,2054:0.998:2058:0,1021:3,851:3,1,1007,1047
chr2 29445982 . G C . clustered_events AS_SB_TABLE=467,521|211,245;ECNT=5;GERMQ=93;SOURCES=mutect2;DP=1549;AS_FilterStatus=SITE;MBQ=38,38;MFRL=214,207;MMQ=60,60;MPOS=16;POPAF=0.401;TLOD=1470.19 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:988,456:0.314:1444:492,241:449,187:467,521,211,245
chr2 29446021 . T C . clustered_events AS_SB_TABLE=540,638|78,94;ECNT=5;GERMQ=93;SOURCES=mutect2;DP=1446;AS_FilterStatus=SITE;MBQ=38,38;MFRL=213,222;MMQ=60,60;MPOS=18;POPAF=7.3;TLOD=475.2 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:1178,172:0.126:1350:519,82:484,61:540,638,78,94
chr2 29446043 . C A . clustered_events AS_SB_TABLE=582,746|37,46;ECNT=5;GERMQ=93;SOURCES=mutect2;DP=1469;AS_FilterStatus=SITE;MBQ=38,38;MFRL=209,216;MMQ=60,60;MPOS=21;POPAF=1.92;TLOD=198.52 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:1328,83:0.059:1411:558,37:499,29:582,746,37,46
chr2 29446128 . A G . clustered_events AS_SB_TABLE=599,512|290,269;ECNT=5;GERMQ=93;SOURCES=mutect2;DP=1796;AS_FilterStatus=SITE;MBQ=38,38;MFRL=206,210;MMQ=60,60;MPOS=20;POPAF=0.917;TLOD=1773.79 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:1111,559:0.329:1670:410,218:351,164:599,512,290,269
chr2 29446184 . C G . clustered_events AS_SB_TABLE=1111,598|126,71;ECNT=5;GERMQ=93;SOURCES=mutect2;DP=1982;AS_FilterStatus=SITE;MBQ=38,38;MFRL=188,183;MMQ=60,60;MPOS=16;POPAF=0.565;TLOD=519.11 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:1709,197:0.105:1906:616,77:620,64:1111,598,126,71
chr2 29446701 . T C . haplotype AS_SB_TABLE=148,43|716,249;ECNT=2;GERMQ=93;SOURCES=mutect2;DP=1211;AS_FilterStatus=SITE;MBQ=38,38;MFRL=238,221;MMQ=60,60;MPOS=18;POPAF=0.4;TLOD=3673.47 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:191,965:0.831:1156:97,540:83,376:0|1:29446701_T_C:29446701:148,43,716,249
chr2 29446721 . A G . germline;haplotype AS_SB_TABLE=60,20|807,311;ECNT=2;GERMQ=1;SOURCES=mutect2;DP=1230;AS_FilterStatus=SITE;MBQ=38,38;MFRL=223,220;MMQ=60,60;MPOS=16;POPAF=0.049;TLOD=4859.97 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:80,1118:0.933:1198:44,558:28,434:0|1:29446701_T_C:29446701:60,20,807,311
chr2 29447108 . G A . PASS AS_SB_TABLE=771,744|143,155;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=1957;AS_FilterStatus=SITE;MBQ=38,38;MFRL=193,202;MMQ=60,60;MPOS=21;POPAF=0.149;TLOD=863.27 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:1515,298:0.167:1813:695,148:703,133:771,744,143,155
chr2 29447253 . A G . germline AS_SB_TABLE=1,1|923,757;ECNT=1;GERMQ=1;SOURCES=mutect2;DP=1793;AS_FilterStatus=SITE;MBQ=23,38;MFRL=275,216;MMQ=60,60;MPOS=16;POPAF=0.271;TLOD=6798.84 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:2,1680:0.999:1682:1,826:0,742:1,1,923,757
chr2 29447605 . T C . PASS AS_SB_TABLE=638,994|67,131;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=1917;AS_FilterStatus=SITE;MBQ=38,38;MFRL=189,201;MMQ=60,60;MPOS=17;POPAF=2.88;TLOD=525.73 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:1632,198:0.107:1830:818,96:684,84:638,994,67,131
chr2 29448206 . C A . PASS AS_SB_TABLE=866,814|59,63;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=1922;AS_FilterStatus=SITE;MBQ=38,38;MFRL=184,189;MMQ=60,60;MPOS=20;POPAF=7.3;TLOD=297.74 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:1680,122:0.069:1802:860,66:662,47:866,814,59,63
chr2 29448760 . C T . PASS AS_SB_TABLE=175,198|529,583;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=1606;AS_FilterStatus=SITE;MBQ=38,38;MFRL=184,197;MMQ=60,60;MPOS=17;POPAF=0.676;TLOD=4191.06 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:373,1112:0.755:1485:211,604:133,447:175,198,529,583
chr2 29448846 . C G 0.851834 LowFisherScore SOMATIC;FETS=0.851834;TYPE=snv;LEN=1;KMERSIZE=31;SB=14.7681;SOURCES=mutect2,lancet GT:AD:SR:SA:DP 0/1:502,109:231,271:58,51:611
chr2 29448873 . C T 0.47961 LowFisherScore SOMATIC;FETS=0.47961;TYPE=snv;LEN=1;KMERSIZE=31;SB=10.9655;SOURCES=mutect2,lancet GT:AD:SR:SA:DP 0/1:864,101:391,473:44,57:965
chr2 29449005 . G T 0 LowFisherScore SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=31;SB=8.56179;SOURCES=mutect2,lancet GT:AD:SR:SA:DP 0/1:487,40:95,392:6,34:527
chr2 29449344 MantaDEL:82:0:0:0:0:0 CAAAAAAAAA C . . END=29449353;SVTYPE=DEL;SVLEN=-9;CIPOS=0,15;HOMLEN=15;HOMSEQ=AAAAAAAAAAAAAAA;UPSTREAM_PAIR_COUNT=0;DOWNSTREAM_PAIR_COUNT=0;PAIR_COUNT=0;CIGAR=1M9D . .
chr2 29449370 . A G . base_qual;clustered_events AS_SB_TABLE=284,12|14,0;ECNT=5;GERMQ=93;SOURCES=mutect2;DP=328;AS_FilterStatus=base_qual;MBQ=31,11;MFRL=237,242;MMQ=60,60;MPOS=17;POPAF=7.3;TLOD=3.75 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:296,14:0.029:310:104,0:110,2:284,12,14,0
chr2 29449373 . A G . base_qual;clustered_events AS_SB_TABLE=274,11|25,0;ECNT=5;GERMQ=93;SOURCES=mutect2;DP=351;AS_FilterStatus=base_qual;MBQ=28,11;MFRL=230,258;MMQ=60,60;MPOS=13;POPAF=3.08;TLOD=9.38 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:285,25:0.057:310:99,2:100,0:274,11,25,0
chr2 29449377 . G A . base_qual;clustered_events AS_SB_TABLE=290,11|33,0;ECNT=5;GERMQ=93;SOURCES=mutect2;DP=355;AS_FilterStatus=base_qual;MBQ=25,11;MFRL=227,240;MMQ=60,60;MPOS=21;POPAF=7.3;TLOD=9.59 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:301,33:0.051:334:100,2:100,2:290,11,33,0
chr2 29449423 . G A 0 LowFisherSTR SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=31;SB=8.17083;MS=9GCT;SOURCES=mutect2 GT:AD:SR:SA:DP 0/1:53,472:44,9:393,79:525
chr2 29449526 . C T 21.8382 LowCovNormal;HighVafNormal;HighAltCntNormal SHARED;FETS=21.8382;TYPE=snv;LEN=1;KMERSIZE=13;SB=11.6293;SOURCES=mutect2,lancet GT:AD:SR:SA:DP 0/1:1130,98:614,516:50,48:1228
chr2 29449697 . C T 4.66271 LowFisherScore SOMATIC;FETS=4.66271;TYPE=snv;LEN=1;KMERSIZE=13;SB=14.1686;SOURCES=mutect2,lancet GT:AD:SR:SA:DP 0/1:1246,537:704,542:309,228:1783
chr2 29449819 . C T 0.912277 LowFisherScore SOMATIC;FETS=0.912277;TYPE=snv;LEN=1;KMERSIZE=13;SB=12.9036;SOURCES=mutect2,lancet GT:AD:SR:SA:DP 0/1:2204,160:1275,929:88,72:2364
chr2 29450122 . G A . PASS AS_SB_TABLE=807,617|381,301;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=2157;AS_FilterStatus=SITE;MBQ=38,38;MFRL=185,171;MMQ=60,60;MPOS=17;POPAF=7.3;TLOD=2092.31 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:1424,682:0.315:2106:702,325:597,273:807,617,381,301
chr2 29450292 . G A . PASS AS_SB_TABLE=650,702|337,330;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=2105;AS_FilterStatus=SITE;MBQ=38,38;MFRL=197,193;MMQ=60,60;MPOS=19;POPAF=7.3;TLOD=2140.14 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:1352,667:0.329:2019:685,334:560,282:650,702,337,330
chr2 29451842 . TG T 0 LowFisherScore SOMATIC;FETS=0;TYPE=del;LEN=1;KMERSIZE=21;SB=7.03774;SOURCES=lancet GT:AD:SR:SA:DP 0/1:318,29:259,59:24,5:347
chr2 29451861 . C T 0.0318945 LowFisherScore;LowVafTumor SOMATIC;FETS=0.0318945;TYPE=snv;LEN=1;KMERSIZE=15;SB=3.88376;SOURCES=lancet GT:AD:SR:SA:DP 0/1:406,3:314,92:2,1:409
chr2 29451972 . A G 0.0300551 LowFisherScore;LowVafTumor;LowAltCntTumor;StrandBias SOMATIC;FETS=0.0300551;TYPE=snv;LEN=1;KMERSIZE=15;SB=1.02117;SOURCES=lancet GT:AD:SR:SA:DP 0/1:287,2:32,255:0,2:289
chr2 29454901 MantaINS:60:0:0:0:0:0 G GCAAGTTGGTAAAACC . . END=29454901;SVTYPE=INS;SVLEN=15;CIPOS=0,2;HOMLEN=2;HOMSEQ=CA;UPSTREAM_PAIR_COUNT=0;DOWNSTREAM_PAIR_COUNT=0;PAIR_COUNT=0;CIGAR=1M15I . .
chr2 29455267 . A G . PASS AS_SB_TABLE=88,121|348,555;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=1156;AS_FilterStatus=SITE;MBQ=38,38;MFRL=152,161;MMQ=60,60;MPOS=17;POPAF=0.2;TLOD=3287.41 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:209,903:0.814:1112:105,447:75,349:88,121,348,555
chr2 29456375 . C T 0 LowFisherScore;LowVafTumor;LowAltCntTumor;StrandBias SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=25;SB=0.260078;SOURCES=lancet GT:AD:SR:SA:DP 0/1:168,2:163,5:2,0:170
chr2 29456383 . TTG TCA 0 LowFisherScore SOMATIC;FETS=0;TYPE=complex;LEN=2;KMERSIZE=15;SB=5.43587;SOURCES=lancet GT:AD:SR:SA:DP 0/1:277,28:254,23:26,2:305
chr2 29456465 . C T 0 LowFisherSTR;LowVafTumor;LowAltCntTumor SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=25;SB=3.39258;MS=9CCT;SOURCES GT:AD:SR:SA:DP 0/1:375,2:243,132:1,1:377
chr2 29456466 . C T 0 LowFisherSTR;LowVafTumor;LowAltCntTumor SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=25;SB=3.31152;MS=10CCT;SOURCES GT:AD:SR:SA:DP 0/1:389,2:246,143:1,1:391
chr2 29462520 . G A . PASS AS_SB_TABLE=553,105|100,21;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=831;AS_FilterStatus=SITE;MBQ=38,38;MFRL=174,174;MMQ=60,60;MPOS=17;POPAF=0.963;TLOD=343.61 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:658,121:0.159:779:318,67:275,44:553,105,100,21
chr2 29462684 . G A . PASS AS_SB_TABLE=334,830|40,79;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=1365;AS_FilterStatus=SITE;MBQ=38,38;MFRL=154,147;MMQ=60,60;MPOS=19;POPAF=4.13;TLOD=297.27 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:1164,119:0.093:1283:546,54:435,47:334,830,40,79
chr2 29498120 MantaBND:66:0:1:0:3:0:0 G G]chr3:137314465] . . SVTYPE=BND;MATEID=MantaBND:66:0:1:0:3:0:1;CIPOS=0,4;HOMLEN=4;HOMSEQ=AGTT;BND_PAIR_COUNT=1;PAIR_COUNT=1 . .
chr2 29498143 . G T . PASS AS_SB_TABLE=508,413|220,230;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=1476;AS_FilterStatus=SITE;MBQ=38,38;MFRL=213,215;MMQ=60,60;MPOS=18;POPAF=7.3;TLOD=1450 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:921,450:0.326:1371:482,242:397,188:508,413,220,230
chr2 29498210 . A G . germline AS_SB_TABLE=46,62|724,589;ECNT=1;GERMQ=1;SOURCES=mutect2;DP=1498;AS_FilterStatus=SITE;MBQ=34,38;MFRL=195,192;MMQ=60,60;MPOS=17;POPAF=0.041;TLOD=5018.79 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:108,1313:0.926:1421:47,719:45,487:46,62,724,589
chr2 29541104 . C T . germline AS_SB_TABLE=443,74|323,57;ECNT=1;GERMQ=1;SOURCES=mutect2;DP=933;AS_FilterStatus=SITE;MBQ=38,38;MFRL=192,190;MMQ=60,60;MPOS=20;POPAF=0.225;TLOD=1268.17 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:517,380:0.423:897:285,214:203,140:443,74,323,57
chr2 29543663 . T C . germline AS_SB_TABLE=41,31|534,485;ECNT=2;GERMQ=1;SOURCES=mutect2;DP=1134;AS_FilterStatus=SITE;MBQ=38,38;MFRL=164,166;MMQ=60,60;MPOS=18;POPAF=0.087;TLOD=3847.97 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:72,1019:0.932:1091:34,489:32,418:41,31,534,485
chr2 29543736 . A G . PASS AS_SB_TABLE=210,391|72,160;ECNT=2;GERMQ=93;SOURCES=mutect2;DP=877;AS_FilterStatus=SITE;MBQ=38,38;MFRL=171,166;MMQ=60,60;MPOS=16;POPAF=1.6;TLOD=698.54 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:601,232:0.274:833:211,80:183,63:210,391,72,160
chr2 29917940 . C G . PASS AS_SB_TABLE=0,62|6,331;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=436;AS_FilterStatus=SITE;MBQ=38,38;MFRL=198,194;MMQ=60,60;MPOS=16;POPAF=0.178;TLOD=1318.68 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:62,337:0.843:399:33,170:27,153:0,62,6,331
chr2 29940529 . A T . PASS AS_SB_TABLE=32,89|138,334;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=650;AS_FilterStatus=SITE;MBQ=38,38;MFRL=170,177;MMQ=60,60;MPOS=20;POPAF=0.178;TLOD=1782.14 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:121,472:0.801:593:56,235:46,194:32,89,138,334
chr2 30143058 . C G . PASS AS_SB_TABLE=286,505|149,244;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=1264;AS_FilterStatus=SITE;MBQ=38,38;MFRL=179,173;MMQ=60,60;MPOS=16;POPAF=7.3;TLOD=1154.38 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:791,393:0.328:1184:365,175:322,156:286,505,149,244
chr2 30143499 . G C . germline AS_SB_TABLE=9,9|44,213;ECNT=1;GERMQ=1;SOURCES=mutect2;DP=294;AS_FilterStatus=SITE;MBQ=37,38;MFRL=164,232;MMQ=60,60;MPOS=17;POPAF=0.051;TLOD=998.16 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:18,257:0.936:275:8,127:8,113:9,9,44,213
chr2 70335208 MantaBND:29:0:1:0:1:0:0 T ]chr1:162723066]T . . SVTYPE=BND;MATEID=MantaBND:29:0:1:0:1:0:1;CIPOS=0,4;HOMLEN=4;HOMSEQ=GGGT;BND_PAIR_COUNT=1;PAIR_COUNT=1 . .
chr2 142328153 MantaDEL:91:0:0:0:0:0 AGTTTGACCTCGGAAGAGG A . . END=142328171;SVTYPE=DEL;SVLEN=-18;CIPOS=0,2;HOMLEN=2;HOMSEQ=GT;UPSTREAM_PAIR_COUNT=0;DOWNSTREAM_PAIR_COUNT=0;PAIR_COUNT=0;CIGAR=1M18D . .
chr2 212251864 . T C . germline AS_SB_TABLE=97,357|61,263;ECNT=1;GERMQ=1;SOURCES=mutect2;DP=828;AS_FilterStatus=SITE;MBQ=38,38;MFRL=185,187;MMQ=60,60;MPOS=22;POPAF=0.553;TLOD=1080.48 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:454,324:0.417:778:230,167:175,119:97,357,61,263
chr2 212252809 . G A . germline AS_SB_TABLE=0,57|0,72;ECNT=1;GERMQ=1;SOURCES=mutect2;DP=153;AS_FilterStatus=SITE;MBQ=38,38;MFRL=260,274;MMQ=60,60;MPOS=17;POPAF=0.208;TLOD=253.3 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:57,72:0.558:129:34,34:22,37:0,57,0,72
chr2 212285103 . T C 0 LowFisherScore;StrandBias SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=17;SB=0;SOURCES=lancet GT:AD:SR:SA:DP 0/1:182,14:182,0:14,0:196
chr2 212285339 . AAAAG A 0 LowFisherScore SOMATIC;FETS=0;TYPE=del;LEN=4;KMERSIZE=13;SB=6.26562;SOURCES=lancet GT:AD:SR:SA:DP 0/1:355,22:40,315:3,19:377
chr2 212293044 . C T . PASS AS_SB_TABLE=133,0|15,0;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=149;AS_FilterStatus=SITE;MBQ=38,38;MFRL=195,217;MMQ=60,60;MPOS=16;POPAF=1.68;TLOD=40.27 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:133,15:0.107:148:84,9:49,6:133,0,15,0
chr2 212295875 . C T . germline AS_SB_TABLE=2,137|1,130;ECNT=1;GERMQ=1;SOURCES=mutect2;DP=275;AS_FilterStatus=SITE;MBQ=38,38;MFRL=235,225;MMQ=60,60;MPOS=24;POPAF=0.122;TLOD=449.52 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:139,131:0.485:270:80,73:57,55:2,137,1,130
chr2 212495028 . C T 0 LowFisherScore;LowVafTumor;LowAltCntTumor;StrandBias SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=17;SB=0;SOURCES=lancet GT:AD:SR:SA:DP 0/1:55,2:55,0:2,0:57
chr2 212495342 . A AT 0 LowFisherScore;StrandBias SOMATIC;FETS=0;TYPE=ins;LEN=1;KMERSIZE=17;SB=0.386294;SOURCES=lancet GT:AD:SR:SA:DP 0/1:129,12:1,128:0,12:141
chr2 212495362 . A G 0 LowFisherScore;StrandBias SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=17;SB=0;SOURCES=mutect2,lancet GT:AD:SR:SA:DP 0/1:160,9:0,160:0,9:169
chr2 212530152 . A G 0.0120303 LowFisherScore;LowVafTumor;LowAltCntTumor;StrandBias SOMATIC;FETS=0.0120303;TYPE=snv;LEN=1;KMERSIZE=17;SB=2.67102;SOURCES=lancet GT:AD:SR:SA:DP 0/1:720,2:191,529:0,2:722
chr2 212530210 . G A 0 LowFisherScore;LowVafTumor;LowAltCntTumor;StrandBias SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=17;SB=1.06274;SOURCES=lancet GT:AD:SR:SA:DP 0/1:259,2:30,229:0,2:261
chr2 212543691 MantaDEL:98:0:0:0:2:0 CAAAAAAAAAA C . . END=212543701;SVTYPE=DEL;SVLEN=-10;CIPOS=0,15;HOMLEN=15;HOMSEQ=AAAAAAAAAAAAAAA;UPSTREAM_PAIR_COUNT=0;DOWNSTREAM_PAIR_COUNT=0;PAIR_COUNT=0;CIGAR=1M10D . .
chr2 212543924 . A G . PASS AS_SB_TABLE=61,355|10,128;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=567;AS_FilterStatus=SITE;MBQ=38,38;MFRL=182,172;MMQ=60,60;MPOS=16;POPAF=0.361;TLOD=439.53 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:416,138:0.255:554:211,68:169,64:61,355,10,128
chr2 212566477 . G A 0 LowFisherScore;StrandBias SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=31;SB=0;SOURCES=lancet GT:AD:SR:SA:DP 0/1:9,8:9,0:8,0:17
chr2 212566481 MantaDEL:99:0:0:0:1:0 CAAAAAAAAAAAA C . . END=212566493;SVTYPE=DEL;SVLEN=-12;CIPOS=0,16;HOMLEN=16;HOMSEQ=AAAAAAAAAAAAAAAA;UPSTREAM_PAIR_COUNT=0;DOWNSTREAM_PAIR_COUNT=0;PAIR_COUNT=0;CIGAR=1M12D . .
chr2 212566644 . GA G 0.359126 LowFisherScore;StrandBias SOMATIC;FETS=0.359126;TYPE=del;LEN=1;KMERSIZE=19;SB=0;SOURCES=lancet GT:AD:SR:SA:DP 0/1:347,30:347,0:30,0:377
chr2 212569983 . G A . germline AS_SB_TABLE=80,2|92,3;ECNT=1;GERMQ=1;SOURCES=mutect2;DP=184;AS_FilterStatus=SITE;MBQ=38,38;MFRL=230,217;MMQ=60,60;MPOS=18;POPAF=0.25;TLOD=338.4 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:82,95:0.534:177:46,43:35,50:80,2,92,3
chr2 212578256 . T C 0 LowFisherScore;LowVafTumor SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=17;SB=3.56236;SOURCES=lancet GT:AD:SR:SA:DP 0/1:451,3:320,131:2,1:454
chr2 212578289 . C T 0 LowFisherScore;LowVafTumor SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=17;SB=5.14284;SOURCES=lancet GT:AD:SR:SA:DP 0/1:692,3:403,289:1,2:695
chr2 212578324 . G A 0 LowFisherScore;LowVafTumor;StrandBias SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=17;SB=6.55932;SOURCES=lancet GT:AD:SR:SA:DP 0/1:673,3:267,406:0,3:676
chr2 212578337 . G A 0 LowFisherScore;LowVafTumor;LowAltCntTumor;StrandBias SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=17;SB=3.27371;SOURCES=lancet GT:AD:SR:SA:DP 0/1:473,2:149,324:0,2:475
chr2 212578366 . A G 0 LowFisherScore;LowVafTumor;LowAltCntTumor;StrandBias SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=17;SB=1.86624;SOURCES=lancet GT:AD:SR:SA:DP 0/1:314,2:61,253:0,2:316
chr2 212578481 . T C 0 LowFisherScore;StrandBias SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=17;SB=0;SOURCES=lancet GT:AD:SR:SA:DP 0/1:69,29:0,69:0,29:98
chr2 212615516 . T C . germline AS_SB_TABLE=0,201|0,283;ECNT=1;GERMQ=1;SOURCES=mutect2;DP=547;AS_FilterStatus=SITE;MBQ=38,38;MFRL=212,205;MMQ=60,60;MPOS=15;POPAF=0.331;TLOD=1039.67 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:201,283:0.584:484:102,155:98,124:0,201,0,283
chr2 212652704 . A T 0 LowFisherScore;LowVafTumor;StrandBias SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=15;SB=0.129002;SOURCES=lancet GT:AD:SR:SA:DP 0/1:201,3:199,2:3,0:204
chr2 212652788 . G A 0 LowFisherScore;LowVafTumor;LowAltCntTumor;StrandBias SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=15;SB=4.22857;SOURCES=lancet GT:AD:SR:SA:DP 0/1:424,2:260,164:2,0:426
chr2 212652789 . A G 0 LowFisherScore;LowVafTumor;LowAltCntTumor;StrandBias SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=15;SB=8.07729;SOURCES=lancet GT:AD:SR:SA:DP 0/1:423,2:257,166:0,2:425
chr2 212652840 . A G 0 LowFisherScore;LowVafTumor;LowAltCntTumor;StrandBias SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=15;SB=3.21429;SOURCES=lancet GT:AD:SR:SA:DP 0/1:380,2:118,262:0,2:382
chr2 212652891 . TA T 0 LowFisherScore;StrandBias SOMATIC;FETS=0;TYPE=del;LEN=1;KMERSIZE=15;SB=1.91504;SOURCES=lancet GT:AD:SR:SA:DP 0/1:180,10:8,172:0,10:190
chr2 212653087 . GA G 0 LowFisherScore;StrandBias SOMATIC;FETS=0;TYPE=del;LEN=1;KMERSIZE=19;SB=0;SOURCES=lancet GT:AD:SR:SA:DP 0/1:34,15:0,34:0,15:49
chr2 213403091 . G A 0 LowFisherScore SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=15;SB=5.25391;SOURCES=mutect2,lancet GT:AD:SR:SA:DP 0/1:133,99:129,4:96,3:232
chr2 213403212 . C T 0 LowFisherScore;LowVafTumor;LowAltCntTumor;StrandBias SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=19;SB=8.77472;SOURCES=lancet GT:AD:SR:SA:DP 0/1:269,2:172,97:0,2:271
chr2 213403306 . TC T 0 LowFisherScore SOMATIC;FETS=0;TYPE=del;LEN=1;KMERSIZE=15;SB=6.11199;SOURCES=lancet GT:AD:SR:SA:DP 0/1:418,24:55,363:3,21:442
chr2 213403318 . G A 0 LowFisherScore;LowVafTumor;LowAltCntTumor;StrandBias SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=19;SB=1.07518;SOURCES=lancet GT:AD:SR:SA:DP 0/1:385,2:45,340:0,2:387
chr2 213403347 . C T 0 LowFisherScore SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=19;SB=7.34749;SOURCES=mutect2,lancet GT:AD:SR:SA:DP 0/1:224,28:14,210:3,25:252
chr2 213403361 . AG A 0 LowFisherScore;StrandBias SOMATIC;FETS=0;TYPE=del;LEN=1;KMERSIZE=15;SB=1.08616;SOURCES=lancet GT:AD:SR:SA:DP 0/1:141,9:4,137:0,9:150
chr2 213403375 . G A 0 LowFisherSTR;LowVafTumor;LowAltCntTumor;StrandBias SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=19;SB=0.232676;MS=9GC;SOURCES GT:AD:SR:SA:DP 0/1:112,2:3,109:0,2:114
chr2 213403466 . G A 0 LowFisherScore;StrandBias SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=19;SB=0;SOURCES=lancet GT:AD:SR:SA:DP 0/1:30,3:0,30:0,3:33
chr3 41266101 . C A 1.66376 LowFisherScore SOMATIC;FETS=1.66376;TYPE=snv;LEN=1;KMERSIZE=13;SB=34.3817;SOURCES=mutect2,lancet GT:AD:SR:SA:DP 0/1:888,415:527,361:208,207:1303
chr3 41266133 . CCTT C 0.85429 LowFisherScore SOMATIC;FETS=0.85429;TYPE=del;LEN=3;KMERSIZE=13;SB=11.4616;SOURCES=lancet GT:AD:SR:SA:DP 0/1:1266,131:654,612:69,62:1397
chr3 41268720 . G A 0 LowFisherScore;LowVafTumor;LowAltCntTumor;StrandBias SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=23;SB=11.0317;SOURCES=lancet GT:AD:SR:SA:DP 0/1:392,2:283,109:0,2:394
chr3 41268751 . C T 0 LowFisherScore;LowVafTumor;LowAltCntTumor SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=23;SB=4.48499;SOURCES=lancet GT:AD:SR:SA:DP 0/1:595,2:458,137:1,1:597
chr3 41268755 . T C 0 LowFisherScore;LowVafTumor;LowAltCntTumor;StrandBias SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=23;SB=2.42113;SOURCES=lancet GT:AD:SR:SA:DP 0/1:611,2:462,149:2,0:613
chr3 41269152 . A T 0 LowFisherScore;StrandBias SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=15;SB=0;SOURCES=lancet GT:AD:SR:SA:DP 0/1:4,11:0,4:0,11:15
chr3 41275562 MantaBND:113:1:2:0:0:0:0 G [chr5:155951770[G . . SVTYPE=BND;MATEID=MantaBND:113:1:2:0:0:0:1;CIPOS=0,7;HOMLEN=7;HOMSEQ=GTGGGAA;BND_PAIR_COUNT=1;PAIR_COUNT=1 . .
chr3 41279188 MantaDEL:119:0:0:0:0:0 CTTTTTTTTT C . . END=41279197;SVTYPE=DEL;SVLEN=-9;CIPOS=0,12;HOMLEN=12;HOMSEQ=TTTTTTTTTTTT;UPSTREAM_PAIR_COUNT=0;DOWNSTREAM_PAIR_COUNT=0;PAIR_COUNT=0;CIGAR=1M9D . .
chr3 50225299 MantaBND:121:0:1:0:1:0:1 T ]chr12:133210937]T . . SVTYPE=BND;MATEID=MantaBND:121:0:1:0:1:0:0;CIPOS=0,4;HOMLEN=4;HOMSEQ=GCTG;BND_PAIR_COUNT=1;PAIR_COUNT=1 . .
chr3 131688894 MantaBND:125:0:1:0:1:0:1 A A[chr8:38283597[ . . SVTYPE=BND;MATEID=MantaBND:125:0:1:0:1:0:0;CIPOS=0,6;HOMLEN=6;HOMSEQ=CTTCCC;BND_PAIR_COUNT=1;PAIR_COUNT=1 . .
chr3 137314461 MantaBND:66:0:1:0:3:0:1 A A]chr2:29498124] . . SVTYPE=BND;MATEID=MantaBND:66:0:1:0:3:0:0;CIPOS=0,4;HOMLEN=4;HOMSEQ=AACT;BND_PAIR_COUNT=1;PAIR_COUNT=1 . .
chr3 178917005 . A G . PASS AS_SB_TABLE=2,180|0,18;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=228;AS_FilterStatus=SITE;MBQ=38,38;MFRL=299,293;MMQ=60,60;MPOS=20;POPAF=0.618;TLOD=45.09 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:182,18:0.092:200:87,8:91,9:2,180,0,18
chr3 178922222 . G T . PASS AS_SB_TABLE=279,10|14,0;ECNT=2;GERMQ=93;SOURCES=mutect2;DP=354;AS_FilterStatus=SITE;MBQ=38,38;MFRL=204,210;MMQ=60,60;MPOS=15;POPAF=0.618;TLOD=33.89 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:289,14:0.05:303:164,7:119,7:279,10,14,0
chr3 178922274 . C A . germline AS_SB_TABLE=152,65|229,74;ECNT=2;GERMQ=1;SOURCES=mutect2;DP=527;AS_FilterStatus=SITE;MBQ=38,38;MFRL=154,173;MMQ=60,60;MPOS=18;POPAF=0.213;TLOD=1078.48 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:217,303:0.6:520:110,156:62,95:152,65,229,74
chr3 178922430 . A G . PASS AS_SB_TABLE=0,70|1,147;ECNT=1;GERMQ=11;SOURCES=mutect2;DP=256;AS_FilterStatus=SITE;MBQ=38,38;MFRL=217,217;MMQ=60,60;MPOS=21;POPAF=0.258;TLOD=559.88 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:70,148:0.676:218:43,91:26,54:0,70,1,147
chr3 178927410 . A G . PASS AS_SB_TABLE=251,225|12,16;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=561;AS_FilterStatus=SITE;MBQ=38,37;MFRL=165,156;MMQ=60,60;MPOS=18;POPAF=1.05;TLOD=59.99 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:476,28:0.054:504:272,14:157,8:251,225,12,16
chr3 178936091 . G A . PASS AS_SB_TABLE=59,47|2,4;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=124;AS_FilterStatus=SITE;MBQ=38,38;MFRL=169,174;MMQ=60,60;MPOS=5;POPAF=7.3;TLOD=11.42 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:106,6:0.057:112:62,4:28,0:59,47,2,4
chr3 178938747 . A T 0 LowFisherSTR;StrandBias SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=17;SB=0;MS=7TAT;SOURCES GT:AD:SR:SA:DP 0/1:26,3:26,0:3,0:29
chr3 178941801 . G A 0 LowFisherScore;LowVafTumor;LowAltCntTumor;StrandBias SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=15;SB=0.13121;SOURCES=lancet GT:AD:SR:SA:DP 0/1:332,2:327,5:2,0:334
chr3 178941966 . G A 0 LowFisherScore;LowVafTumor;LowAltCntTumor;StrandBias SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=15;SB=1.53454;SOURCES=lancet GT:AD:SR:SA:DP 0/1:369,2:60,309:0,2:371
chr3 178942431 . C G . germline AS_SB_TABLE=22,0|54,0;ECNT=1;GERMQ=1;SOURCES=mutect2;DP=80;AS_FilterStatus=SITE;MBQ=38,38;MFRL=222,215;MMQ=60,60;MPOS=24;POPAF=0.193;TLOD=208.3 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:22,54:0.705:76:13,32:9,22:22,0,54,0
chr3 178947865 . G A . PASS AS_SB_TABLE=340,348|151,153;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=1056;AS_FilterStatus=SITE;MBQ=38,38;MFRL=175,167;MMQ=60,60;MPOS=20;POPAF=7.3;TLOD=918.81 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:688,304:0.304:992:380,165:241,97:340,348,151,153
chr3 178952085 . A G . PASS AS_SB_TABLE=154,499|26,93;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=843;AS_FilterStatus=SITE;MBQ=38,38;MFRL=200,206;MMQ=60,60;MPOS=22;POPAF=7.3;TLOD=350.15 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:653,119:0.158:772:358,62:248,52:154,499,26,93
chr3 181430503 . C G . PASS AS_SB_TABLE=556,483|76,44;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=1260;AS_FilterStatus=SITE;MBQ=38,38;MFRL=204,230;MMQ=60,60;MPOS=20;POPAF=7.3;TLOD=329.59 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:1039,120:0.107:1159:489,56:466,57:556,483,76,44
chr4 1615176 . G C . clustered_events;germline AS_SB_TABLE=0,0|258,88;ECNT=3;GERMQ=1;SOURCES=mutect2;DP=361;AS_FilterStatus=SITE;MBQ=0,38;MFRL=0,192;MMQ=60,60;MPOS=17;POPAF=0.037;TLOD=1390.04 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:0,346:0.997:346:0,190:0,132:0,0,258,88
chr4 1615199 . A G . clustered_events AS_SB_TABLE=62,19|238,100;ECNT=3;GERMQ=93;SOURCES=mutect2;DP=439;AS_FilterStatus=SITE;MBQ=38,38;MFRL=178,184;MMQ=60,60;MPOS=18;POPAF=0.582;TLOD=1283.24 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:81,338:0.806:419:38,174:36,127:62,19,238,100
chr4 1615251 . C T . clustered_events AS_SB_TABLE=62,46|214,189;ECNT=3;GERMQ=93;SOURCES=mutect2;DP=541;AS_FilterStatus=SITE;MBQ=38,38;MFRL=177,170;MMQ=60,60;MPOS=20;POPAF=0.686;TLOD=1442.68 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:108,403:0.79:511:43,172:35,108:62,46,214,189
chr4 1638001 . A G . PASS AS_SB_TABLE=20,28|165,209;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=443;AS_FilterStatus=SITE;MBQ=38,38;MFRL=155,158;MMQ=60,60;MPOS=20;POPAF=0.434;TLOD=1345.01 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:48,374:0.885:422:20,175:19,140:20,28,165,209
chr4 1647598 . A G . clustered_events;germline;haplotype AS_SB_TABLE=25,21|257,303;ECNT=3;GERMQ=1;SOURCES=mutect2;DP=627;AS_FilterStatus=SITE;MBQ=38,38;MFRL=163,164;MMQ=60,60;MPOS=19;POPAF=0.53;TLOD=2428.26 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:46,560:0.923:606:22,291:17,201:0|1:1647598_A_G:1647598:25,21,257,303
chr4 1647600 . A C . clustered_events;germline;haplotype AS_SB_TABLE=25,21|257,303;ECNT=3;GERMQ=1;SOURCES=mutect2;DP=644;AS_FilterStatus=SITE;MBQ=38,38;MFRL=163,164;MMQ=60,60;MPOS=20;POPAF=0.437;TLOD=2428.25 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:46,560:0.923:606:21,299:17,200:0|1:1647598_A_G:1647598:25,21,257,303
chr4 1647654 . C T . clustered_events AS_SB_TABLE=214,425|19,36;ECNT=3;GERMQ=93;SOURCES=mutect2;DP=706;AS_FilterStatus=SITE;MBQ=38,38;MFRL=167,166;MMQ=60,60;MPOS=18;POPAF=7.3;TLOD=139.81 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:639,55:0.084:694:257,22:205,17:214,425,19,36
chr4 1653352 . T C 0 LowFisherScore SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=23;SB=6.94911;SOURCES=mutect2,lancet GT:AD:SR:SA:DP 0/1:27,198:22,5:158,40:225
chr4 1653452 . C T 0 LowFisherScore;LowVafTumor SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=23;SB=3.53557;SOURCES=lancet GT:AD:SR:SA:DP 0/1:226,3:84,142:1,2:229
chr4 1707447 . T C . germline AS_SB_TABLE=117,213|118,194;ECNT=1;GERMQ=1;SOURCES=mutect2;DP=644;AS_FilterStatus=SITE;MBQ=38,38;MFRL=173,177;MMQ=60,60;MPOS=19;POPAF=0.117;TLOD=1056.22 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:330,312:0.49:642:176,158:118,124:117,213,118,194
chr4 1720757 . A G . germline AS_SB_TABLE=177,41|156,45;ECNT=2;GERMQ=1;SOURCES=mutect2;DP=435;AS_FilterStatus=SITE;MBQ=38,38;MFRL=194,196;MMQ=60,60;MPOS=17;POPAF=0.145;TLOD=701.49 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:218,201:0.483:419:115,104:87,90:177,41,156,45
chr4 1720824 . A G . germline AS_SB_TABLE=93,126|77,124;ECNT=2;GERMQ=1;SOURCES=mutect2;DP=454;AS_FilterStatus=SITE;MBQ=38,38;MFRL=180,184;MMQ=60,60;MPOS=16;POPAF=0.145;TLOD=677.07 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:219,201:0.475:420:102,80:45,54:93,126,77,124
chr4 1729154 . G A 0 LowFisherScore;StrandBias SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=13;SB=0;SOURCES=lancet GT:AD:SR:SA:DP 0/1:6,9:6,0:9,0:15
chr4 1729346 . AAT AGA 0 LowFisherScore SOMATIC;FETS=0;TYPE=complex;LEN=2;KMERSIZE=13;SB=8.85574;SOURCES=lancet GT:AD:SR:SA:DP 0/1:167,123:143,24:107,16:290
chr4 1729425 . C G 0 LowFisherScore SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=13;SB=17.6009;SOURCES=mutect2,lancet GT:AD:SR:SA:DP 0/1:227,225:109,118:90,135:452
chr4 1729556 . G A 0 LowFisherScore SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=13;SB=10.7704;SOURCES=lancet GT:AD:SR:SA:DP 0/1:110,48:10,100:1,47:158
chr4 1737585 . T C . germline AS_SB_TABLE=288,283|290,261;ECNT=1;GERMQ=1;SOURCES=mutect2;DP=1204;AS_FilterStatus=SITE;MBQ=38,38;MFRL=162,157;MMQ=60,60;MPOS=17;POPAF=0.135;TLOD=1769.62 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:571,551:0.484:1122:258,245:242,214:288,283,290,261
chr4 1788130 . C G . germline AS_SB_TABLE=123,149|79,111;ECNT=1;GERMQ=1;SOURCES=mutect2;DP=501;AS_FilterStatus=SITE;MBQ=38,38;MFRL=153,165;MMQ=60,60;MPOS=19;POPAF=0.553;TLOD=621.47 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:272,190:0.418:462:153,96:86,74:123,149,79,111
chr4 1795557 . T C . germline AS_SB_TABLE=0,0|54,1;ECNT=1;GERMQ=1;SOURCES=mutect2;DP=58;AS_FilterStatus=SITE;MBQ=0,38;MFRL=0,276;MMQ=60,60;MPOS=19;POPAF=0.001305;TLOD=222.81 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:0,55:0.983:55:0,28:0,27:0,0,54,1
chr4 1801137 . TG T 0 LowFisherScore SOMATIC;FETS=0;TYPE=del;LEN=1;KMERSIZE=15;SB=13.241;SOURCES=lancet GT:AD:SR:SA:DP 0/1:1024,377:532,492:194,183:1401
chr4 1801363 . G C 0 LowFisherScore SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=15;SB=10.3153;SOURCES=mutect2,lancet GT:AD:SR:SA:DP 0/1:866,81:488,378:46,35:947
chr4 1803307 . T C . PASS AS_SB_TABLE=571,356|239,191;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=1418;AS_FilterStatus=SITE;MBQ=38,38;MFRL=167,170;MMQ=60,60;MPOS=17;POPAF=0.701;TLOD=1405.68 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:927,430:0.325:1357:544,227:309,181:571,356,239,191
chr4 1803474 . A G . clustered_events;strand_bias AS_SB_TABLE=299,592|2,51;ECNT=5;GERMQ=93;SOURCES=mutect2;DP=1045;AS_FilterStatus=strand_bias;MBQ=38,21;MFRL=192,174;MMQ=60,60;MPOS=21;POPAF=7.3;TLOD=38.2 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:891,53:0.036:944:403,9:311,5:299,592,2,51
chr4 1803481 . T G . clustered_events;strand_bias AS_SB_TABLE=324,508|0,59;ECNT=5;GERMQ=93;SOURCES=mutect2;DP=945;AS_FilterStatus=strand_bias;MBQ=38,22;MFRL=198,176;MMQ=60,60;MPOS=18;POPAF=7.3;TLOD=42.64 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:832,59:0.045:891:366,13:298,7:324,508,0,59
chr4 1803486 . C G . base_qual;clustered_events;strand_bias AS_SB_TABLE=324,484|0,33;ECNT=5;GERMQ=93;SOURCES=mutect2;DP=912;AS_FilterStatus=base_qual;MBQ=38,10;MFRL=203,202;MMQ=60,60;MPOS=18;POPAF=7.3;TLOD=3.97 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:808,33:0.012:841:343,4:284,2:324,484,0,33
chr4 1803491 . C G . clustered_events;strand_bias AS_SB_TABLE=314,384|0,66;ECNT=5;GERMQ=93;SOURCES=mutect2;DP=826;AS_FilterStatus=strand_bias;MBQ=35,22;MFRL=207,188;MMQ=60,60;MPOS=15;POPAF=7.3;TLOD=32.99 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:698,66:0.05:764:305,8:254,10:314,384,0,66
chr4 1803497 . T G . clustered_events;strand_bias AS_SB_TABLE=328,319|0,62;ECNT=5;GERMQ=93;SOURCES=mutect2;DP=765;AS_FilterStatus=strand_bias;MBQ=36,22;MFRL=209,192;MMQ=60,60;MPOS=13;POPAF=7.3;TLOD=50.04 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:647,62:0.051:709:265,8:228,12:328,319,0,62
chr4 1803704 . T C . PASS AS_SB_TABLE=538,680|313,356;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=1968;AS_FilterStatus=SITE;MBQ=38,38;MFRL=160,163;MMQ=60,60;MPOS=18;POPAF=0.728;TLOD=2117.79 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:1218,669:0.357:1887:585,339:467,246:538,680,313,356
chr4 1803824 . C G . PASS AS_SB_TABLE=298,511|145,299;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=1289;AS_FilterStatus=SITE;MBQ=38,38;MFRL=170,173;MMQ=60,60;MPOS=20;POPAF=0.728;TLOD=1365.12 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:809,444:0.355:1253:403,234:301,153:298,511,145,299
chr4 1805593 . G C 0.453541 LowFisherScore SOMATIC;FETS=0.453541;TYPE=snv;LEN=1;KMERSIZE=19;SB=11.5272;SOURCES=mutect2,lancet GT:AD:SR:SA:DP 0/1:753,83:341,412:34,49:836
chr4 1806436 . T G 0 LowFisherScore SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=15;SB=10.6608;SOURCES=mutect2,lancet GT:AD:SR:SA:DP 0/1:760,50:438,322:26,24:810
chr4 1806519 . C T 1.77354 LowFisherScore SOMATIC;FETS=1.77354;TYPE=snv;LEN=1;KMERSIZE=15;SB=12.4425;SOURCES=mutect2,lancet GT:AD:SR:SA:DP 0/1:457,231:305,152:149,82:688
chr4 1806834 . G C . germline AS_SB_TABLE=0,0|285,736;ECNT=1;GERMQ=1;SOURCES=mutect2;DP=1057;AS_FilterStatus=SITE;MBQ=0,38;MFRL=0,183;MMQ=60,60;MPOS=17;POPAF=0.012;TLOD=3980.05 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:0,1021:0.999:1021:0,519:0,391:0,0,285,736
chr4 1807894 . G A . germline AS_SB_TABLE=0,1|894,1108;ECNT=1;GERMQ=1;SOURCES=mutect2;DP=2131;AS_FilterStatus=SITE;MBQ=11,38;MFRL=287,174;MMQ=60,60;MPOS=19;POPAF=0.015;TLOD=7762.39 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:1,2002:0.999:2003:0,955:0,797:0,1,894,1108
chr4 1809127 . C T 0.160344 LowFisherSTR;LowVafTumor SOMATIC;FETS=0.160344;TYPE=snv;LEN=1;KMERSIZE=35;SB=10.0193;MS=18TG;SOURCES GT:AD:SR:SA:DP 0/1:903,34:463,440:15,19:937
chr4 1809129 . T C 0.413042 LowFisherSTR SOMATIC;FETS=0.413042;TYPE=snv;LEN=1;KMERSIZE=35;SB=12.3514;MS=17TGGT;SOURCES=mutect2 GT:AD:SR:SA:DP 0/1:891,89:446,445:40,49:980
chr4 1809728 . TG T 0.530567 LowFisherScore SOMATIC;FETS=0.530567;TYPE=del;LEN=1;KMERSIZE=21;SB=7.02662;SOURCES=lancet GT:AD:SR:SA:DP 0/1:353,46:329,24:42,4:399
chr4 1809787 . C T 0 LowFisherScore SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=17;SB=0;SOURCES=mutect2,lancet GT:AD:SR:SA:DP 1/1:0,859:0,0:649,210:859
chr4 1809907 . C T 0 LowFisherScore SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=15;SB=11.0475;SOURCES=mutect2,lancet GT:AD:SR:SA:DP 0/1:1158,107:721,437:65,42:1265
chr4 1821924 . C T . PASS AS_SB_TABLE=278,8|76,1;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=397;AS_FilterStatus=SITE;MBQ=38,38;MFRL=217,227;MMQ=60,60;MPOS=18;POPAF=7.3;TLOD=236.29 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:286,77:0.214:363:137,34:146,42:278,8,76,1
chr4 1834447 . G C . PASS AS_SB_TABLE=96,483|4,45;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=645;AS_FilterStatus=SITE;MBQ=38,38;MFRL=195,185;MMQ=60,60;MPOS=19;POPAF=1.6;TLOD=123.27 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:579,49:0.081:628:323,21:203,26:96,483,4,45
chr4 1863703 . C T 0 LowFisherScore;LowVafTumor;LowAltCntTumor;StrandBias SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=13;SB=0.314745;SOURCES=lancet GT:AD:SR:SA:DP 0/1:139,2:134,5:2,0:141
chr4 1863798 . G T 2.92257 LowFisherScore SOMATIC;FETS=2.92257;TYPE=snv;LEN=1;KMERSIZE=13;SB=11.5653;SOURCES=mutect2,lancet GT:AD:SR:SA:DP 0/1:196,79:107,89:48,31:275
chr4 1864147 . C G 0 LowFisherScore;StrandBias SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=13;SB=0;SOURCES=lancet GT:AD:SR:SA:DP 0/1:1,14:0,1:0,14:15
chr4 1870365 . TC T 0 LowFisherScore SOMATIC;FETS=0;TYPE=del;LEN=1;KMERSIZE=23;SB=12.9452;SOURCES=lancet GT:AD:SR:SA:DP 0/1:484,45:318,166:25,20:529
chr4 1870500 . G A 0 LowFisherScore;LowVafTumor;StrandBias SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=15;SB=3.7018;SOURCES=lancet GT:AD:SR:SA:DP 0/1:746,3:185,561:0,3:749
chr4 1878985 . AT A 0 LowFisherScore SOMATIC;FETS=0;TYPE=del;LEN=1;KMERSIZE=17;SB=7.64844;SOURCES=lancet GT:AD:SR:SA:DP 0/1:484,34:428,56:29,5:518
chr4 1893651 . A G . germline AS_SB_TABLE=81,15|46,10;ECNT=1;GERMQ=1;SOURCES=mutect2;DP=175;AS_FilterStatus=SITE;MBQ=38,37;MFRL=175,187;MMQ=60,60;MPOS=9;POPAF=1.62;TLOD=162.21 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:96,56:0.352:152:51,22:38,25:81,15,46,10
chr4 1909342 MantaDEL:142:0:0:0:0:0 CTTTTTTTTT C . . END=1909351;SVTYPE=DEL;SVLEN=-9;CIPOS=0,14;HOMLEN=14;HOMSEQ=TTTTTTTTTTTTTT;UPSTREAM_PAIR_COUNT=0;DOWNSTREAM_PAIR_COUNT=0;PAIR_COUNT=0;CIGAR=1M9D . .
chr4 1927106 . C T . base_qual AS_SB_TABLE=18,263|0,26;ECNT=2;GERMQ=93;SOURCES=mutect2;DP=319;AS_FilterStatus=base_qual;MBQ=34,10;MFRL=228,246;MMQ=60,40;MPOS=13;POPAF=7.3;TLOD=4.34 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:281,26:0.039:307:87,3:67,0:18,263,0,26
chr4 1927119 MantaDEL:138:0:0:0:2:0 TTTTTTTTT TC . . END=1927127;SVTYPE=DEL;SVLEN=-8;UPSTREAM_PAIR_COUNT=0;DOWNSTREAM_PAIR_COUNT=0;PAIR_COUNT=0;CIGAR=1M1I8D . .
chr4 1927127 . T C 0 LowFisherSTR SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=33;SB=4.6493;MS=16TTTCT;SOURCES GT:AD:SR:SA:DP 0/1:77,65:1,76:2,63:142
chr4 1927128 . T C 0 LowFisherSTR SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=33;SB=6.82414;MS=15TTTCT;SOURCES GT:AD:SR:SA:DP 0/1:77,65:0,77:2,63:142
chr4 1927129 . T C 0 LowFisherSTR SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=33;SB=3.50623;MS=14TTTCT;SOURCES GT:AD:SR:SA:DP 0/1:77,62:0,77:1,61:139
chr4 1927130 . T C 0 LowFisherSTR SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=33;SB=6.82414;MS=13TTTCT;SOURCES GT:AD:SR:SA:DP 0/1:77,65:0,77:2,63:142
chr4 1927131 . T C 0 LowFisherSTR SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=33;SB=6.7005;MS=12TTTCT;SOURCES GT:AD:SR:SA:DP 0/1:75,65:0,75:2,63:140
chr4 1957418 . AG A 0 LowFisherScore SOMATIC;FETS=0;TYPE=del;LEN=1;KMERSIZE=13;SB=8.6147;SOURCES=lancet GT:AD:SR:SA:DP 0/1:535,33:213,322:14,19:568
chr4 1957720 . G A 0 LowFisherScore;StrandBias SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=13;SB=0;SOURCES=lancet GT:AD:SR:SA:DP 0/1:23,20:0,23:0,20:43
chr4 1980886 . C T 0 LowFisherScore;LowVafTumor;LowAltCntTumor;StrandBias SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=15;SB=1.20182;SOURCES=lancet GT:AD:SR:SA:DP 0/1:517,2:450,67:2,0:519
chr4 1980932 . AT A 0.38211 LowFisherScore SOMATIC;FETS=0.38211;TYPE=del;LEN=1;KMERSIZE=13;SB=9.96379;SOURCES=lancet GT:AD:SR:SA:DP 0/1:684,63:451,233:40,23:747
chr4 1980957 . C T 0.668935 LowFisherScore SOMATIC;FETS=0.668935;TYPE=snv;LEN=1;KMERSIZE=13;SB=12.4097;SOURCES=mutect2,lancet GT:AD:SR:SA:DP 0/1:698,56:430,268:39,17:754
chr4 1981165 . AT A 0 LowFisherScore SOMATIC;FETS=0;TYPE=del;LEN=1;KMERSIZE=13;SB=10.3468;SOURCES=lancet GT:AD:SR:SA:DP 0/1:708,69:401,307:41,28:777
chr4 1990425 . A G . PASS AS_SB_TABLE=10,21|43,55;ECNT=1;GERMQ=35;SOURCES=mutect2;DP=150;AS_FilterStatus=SITE;MBQ=38,38;MFRL=182,204;MMQ=60,60;MPOS=18;POPAF=0.593;TLOD=377.18 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:31,98:0.756:129:17,61:14,34:10,21,43,55
chr4 3620553 MantaDEL:135:0:0:0:0:0 CCATCAGATCTTGTGAGAACT C . . END=3620573;SVTYPE=DEL;SVLEN=-20;CIPOS=0,2;HOMLEN=2;HOMSEQ=CA;UPSTREAM_PAIR_COUNT=0;DOWNSTREAM_PAIR_COUNT=0;PAIR_COUNT=0;CIGAR=1M20D . .
chr4 25664244 . G A . PASS AS_SB_TABLE=915,435|76,43;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=1512;AS_FilterStatus=SITE;MBQ=38,38;MFRL=177,170;MMQ=60,60;MPOS=17;POPAF=1.28;TLOD=300.71 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:1350,119:0.08:1469:633,55:594,50:915,435,76,43
chr4 25665812 . A C . base_qual;clustered_events;strand_bias AS_SB_TABLE=261,80|73,1;ECNT=4;GERMQ=93;SOURCES=mutect2;DP=500;AS_FilterStatus=base_qual;MBQ=34,11;MFRL=185,201;MMQ=60,60;MPOS=21;POPAF=2.61;TLOD=50.33 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:341,74:0.124:415:79,17:150,5:261,80,73,1
chr4 25665822 . A C . base_qual;clustered_events;strand_bias AS_SB_TABLE=398,110|53,0;ECNT=4;GERMQ=93;SOURCES=mutect2;DP=646;AS_FilterStatus=base_qual;MBQ=38,11;MFRL=174,184;MMQ=60,60;MPOS=21;POPAF=7.3;TLOD=19.27 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:508,53:0.054:561:167,10:220,4:398,110,53,0
chr4 25666099 . A G 0 LowFisherScore SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=11;SB=5.12708;SOURCES=lancet GT:AD:SR:SA:DP 0/1:72,90:0,72:2,88:162
chr4 25667721 . G T . PASS AS_SB_TABLE=788,156|78,16;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=1097;AS_FilterStatus=SITE;MBQ=38,38;MFRL=172,191;MMQ=60,60;MPOS=14;POPAF=7.3;TLOD=246.97 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:944,94:0.092:1038:448,50:424,39:788,156,78,16
chr4 25669530 . T C . PASS AS_SB_TABLE=758,764|92,104;ECNT=2;GERMQ=93;SOURCES=mutect2;DP=1796;AS_FilterStatus=SITE;MBQ=38,38;MFRL=184,177;MMQ=60,60;MPOS=17;POPAF=1.66;TLOD=513.46 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:1522,196:0.112:1718:793,101:600,73:758,764,92,104
chr4 25669563 . C A . PASS AS_SB_TABLE=788,756|83,72;ECNT=2;GERMQ=93;SOURCES=mutect2;DP=1784;AS_FilterStatus=SITE;MBQ=38,38;MFRL=181,184;MMQ=60,60;MPOS=18;POPAF=7.3;TLOD=403.24 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:1544,155:0.091:1699:768,82:547,47:788,756,83,72
chr4 25674458 . C T 0 LowFisherScore;StrandBias SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=15;SB=0;SOURCES=lancet GT:AD:SR:SA:DP 0/1:11,14:11,0:14,0:25
chr4 25674905 . TCACA T 0 LowFisherScore SOMATIC;FETS=0;TYPE=del;LEN=4;KMERSIZE=15;SB=0;SOURCES=lancet GT:AD:SR:SA:DP 1/1:0,584:0,0:77,507:584
chr4 25674905 MantaDEL:157:1:1:0:0:0 TCACATGTA TTGAGGGATG . . END=25674913;SVTYPE=DEL;SVLEN=9;UPSTREAM_PAIR_COUNT=0;DOWNSTREAM_PAIR_COUNT=0;PAIR_COUNT=0;CIGAR=1M9I8D . .
chr4 25674911 . G GAGGGA 0 LowFisherScore SOMATIC;FETS=0;TYPE=ins;LEN=5;KMERSIZE=15;SB=0;SOURCES=lancet GT:AD:SR:SA:DP 1/1:0,516:0,0:59,457:516
chr4 25674911 . G GTGGGA 0 LowFisherScore;LowCovTumor;LowAltCntTumor;StrandBias SOMATIC;FETS=0;TYPE=ins;LEN=5;KMERSIZE=15;SB=0;SOURCES=lancet GT:AD:SR:SA:DP 1/1:0,2:0,0:0,2:2
chr4 25674913 . A G 0 LowFisherScore SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=15;SB=0;SOURCES=mutect2,lancet GT:AD:SR:SA:DP 1/1:0,644:0,0:86,558:644
chr4 25674999 . C G 0 LowFisherSTR;StrandBias SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=15;SB=0.774815;MS=9CAG;SOURCES GT:AD:SR:SA:DP 0/1:128,25:1,127:0,25:153
chr4 25675860 . G A . PASS AS_SB_TABLE=585,28|283,9;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=946;AS_FilterStatus=SITE;MBQ=38,38;MFRL=202,199;MMQ=60,60;MPOS=19;POPAF=7.3;TLOD=960.77 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:613,292:0.325:905:311,131:275,154:585,28,283,9
chr4 25676109 MantaBND:158:0:1:0:1:0:0 G [chr8:110223395[G . . SVTYPE=BND;MATEID=MantaBND:158:0:1:0:1:0:1;CIPOS=0,6;HOMLEN=6;HOMSEQ=TTTTGT;BND_PAIR_COUNT=1;PAIR_COUNT=1 . .
chr4 25677789 . C T . PASS AS_SB_TABLE=335,151|145,37;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=696;AS_FilterStatus=SITE;MBQ=38,38;MFRL=157,161;MMQ=60,60;MPOS=21;POPAF=4.61;TLOD=550.1 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:486,182:0.274:668:247,101:169,60:335,151,145,37
chr4 25677883 . G A . PASS AS_SB_TABLE=343,386|39,46;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=840;AS_FilterStatus=SITE;MBQ=38,38;MFRL=162,145;MMQ=60,60;MPOS=18;POPAF=7.3;TLOD=209.3 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:729,85:0.102:814:511,42:112,29:343,386,39,46
chr4 25678199 . A G . germline AS_SB_TABLE=1,0|375,720;ECNT=1;GERMQ=1;SOURCES=mutect2;DP=1118;AS_FilterStatus=SITE;MBQ=27,38;MFRL=171,198;MMQ=60,60;MPOS=19;POPAF=0.051;TLOD=4421.66 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:1,1095:0.998:1096:0,546:1,451:1,0,375,720
chr4 25678396 . G T . PASS AS_SB_TABLE=270,627|26,72;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=1025;AS_FilterStatus=SITE;MBQ=38,38;MFRL=165,174;MMQ=60,60;MPOS=17;POPAF=0.599;TLOD=240.33 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:897,98:0.1:995:447,47:317,37:270,627,26,72
chr4 27964519 MantaBND:149:0:1:0:0:0:1 G ]chr6:117674205]G . . SVTYPE=BND;MATEID=MantaBND:149:0:1:0:0:0:0;CIPOS=0,5;HOMLEN=5;HOMSEQ=CCTTT;BND_PAIR_COUNT=1;PAIR_COUNT=1 . .
chr4 55125058 . A T . PASS AS_SB_TABLE=50,542|10,54;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=674;AS_FilterStatus=SITE;MBQ=38,38;MFRL=199,178;MMQ=60,60;MPOS=17;POPAF=0.642;TLOD=160.96 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:592,64:0.092:656:318,28:250,29:50,542,10,54
chr4 55127413 . C T . PASS AS_SB_TABLE=601,488|50,52;ECNT=2;GERMQ=93;SOURCES=mutect2;DP=1267;AS_FilterStatus=SITE;MBQ=38,38;MFRL=191,199;MMQ=60,60;MPOS=22;POPAF=2.38;TLOD=274.79 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:1089,102:0.089:1191:541,52:478,47:601,488,50,52
chr4 55127494 . C T . PASS AS_SB_TABLE=395,790|23,50;ECNT=2;GERMQ=93;SOURCES=mutect2;DP=1326;AS_FilterStatus=SITE;MBQ=38,38;MFRL=169,168;MMQ=60,60;MPOS=15;POPAF=4.61;TLOD=182.42 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:1185,73:0.062:1258:406,25:361,24:395,790,23,50
chr4 55130078 . T C 0 LowFisherScore SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=19;SB=23.3557;SOURCES=mutect2,lancet GT:AD:SR:SA:DP 0/1:918,90:286,632:17,73:1008
chr4 55130154 . G A 0 LowFisherScore SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=19;SB=6.45191;SOURCES=mutect2,lancet GT:AD:SR:SA:DP 0/1:386,28:43,343:2,26:414
chr4 55131129 . G A . PASS AS_SB_TABLE=583,287|43,26;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=975;AS_FilterStatus=SITE;MBQ=38,38;MFRL=175,187;MMQ=60,60;MPOS=13;POPAF=2.27;TLOD=174.99 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:870,69:0.077:939:419,39:341,25:583,287,43,26
chr4 55133726 . T G 0 LowFisherScore SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=15;SB=11.4362;SOURCES=mutect2,lancet GT:AD:SR:SA:DP 0/1:1136,76:622,514:45,31:1212
chr4 55133936 . CT C 0 LowFisherScore SOMATIC;FETS=0;TYPE=del;LEN=1;KMERSIZE=15;SB=12.229;SOURCES=lancet GT:AD:SR:SA:DP 0/1:446,179:56,390:28,151:625
chr4 55133959 . C T 0 LowFisherScore SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=15;SB=6.04097;SOURCES=mutect2,lancet GT:AD:SR:SA:DP 0/1:417,28:33,384:1,27:445
chr4 55133966 . A G 0 LowFisherScore;LowVafTumor;LowAltCntTumor;StrandBias SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=15;SB=0.44018;SOURCES=lancet GT:AD:SR:SA:DP 0/1:383,2:19,364:0,2:385
chr4 55134013 . T A 0 LowFisherScore;LowVafTumor;LowAltCntTumor;StrandBias SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=15;SB=0;SOURCES=lancet GT:AD:SR:SA:DP 0/1:326,2:0,326:0,2:328
chr4 55138600 . G A . PASS AS_SB_TABLE=559,554|251,226;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=1670;AS_FilterStatus=SITE;MBQ=38,38;MFRL=162,168;MMQ=60,60;MPOS=19;POPAF=7.3;TLOD=1446.69 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:1113,477:0.3:1590:518,239:427,172:559,554,251,226
chr4 55139771 . T C . PASS AS_SB_TABLE=618,588|40,50;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=1375;AS_FilterStatus=SITE;MBQ=38,38;MFRL=163,168;MMQ=60,60;MPOS=19;POPAF=0.845;TLOD=209.96 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:1206,90:0.069:1296:599,46:445,29:618,588,40,50
chr4 55141055 . A G . germline AS_SB_TABLE=0,0|615,568;ECNT=1;GERMQ=1;SOURCES=mutect2;DP=1268;AS_FilterStatus=SITE;MBQ=0,38;MFRL=0,171;MMQ=60,60;MPOS=17;POPAF=0.012;TLOD=4618.56 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:0,1183:0.999:1183:0,575:0,498:0,0,615,568
chr4 55143577 . G A . PASS AS_SB_TABLE=668,526|114,79;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=1414;AS_FilterStatus=SITE;MBQ=38,38;MFRL=171,180;MMQ=60,60;MPOS=20;POPAF=0.801;TLOD=527.53 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:1194,193:0.14:1387:585,96:465,75:668,526,114,79
chr4 55144402 MantaDEL:171:0:0:0:0:0 AAAAAAAAAAAAAAAAAAA AG . . END=55144420;SVTYPE=DEL;SVLEN=-18;UPSTREAM_PAIR_COUNT=0;DOWNSTREAM_PAIR_COUNT=0;PAIR_COUNT=0;CIGAR=1M1I18D . .
chr4 55146406 MantaINS:163:0:0:0:0:0 T TTGTAGGTCCCCCAG . . END=55146406;SVTYPE=INS;SVLEN=14;UPSTREAM_PAIR_COUNT=0;DOWNSTREAM_PAIR_COUNT=0;PAIR_COUNT=0;CIGAR=1M14I . .
chr4 55151711 . C A 0 LowFisherScore SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=15;SB=0;SOURCES=mutect2,lancet GT:AD:SR:SA:DP 1/1:0,506:0,0:42,464:506
chr4 55151958 . T TA 0 LowFisherScore SOMATIC;FETS=0;TYPE=ins;LEN=1;KMERSIZE=15;SB=8.02406;SOURCES=lancet GT:AD:SR:SA:DP 0/1:161,583:153,8:557,26:744
chr4 55152040 . C T 4.32589 LowFisherScore SOMATIC;FETS=4.32589;TYPE=snv;LEN=1;KMERSIZE=15;SB=12.1677;SOURCES=mutect2,lancet GT:AD:SR:SA:DP 0/1:990,152:550,440:81,71:1142
chr4 55152284 . T G 0 LowFisherScore;StrandBias SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=15;SB=7.78151;SOURCES=lancet GT:AD:SR:SA:DP 0/1:16,80:1,15:0,80:96
chr4 55154891 . T C . PASS AS_SB_TABLE=650,82|133,8;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=918;AS_FilterStatus=SITE;MBQ=38,38;MFRL=195,192;MMQ=60,60;MPOS=13;POPAF=0.728;TLOD=419.48 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:732,141:0.164:873:406,71:297,66:650,82,133,8
chr4 55161119 . A G 0 LowFisherScore;StrandBias SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=19;SB=2.06474;SOURCES=lancet GT:AD:SR:SA:DP 0/1:46,28:45,1:28,0:74
chr4 55161254 . C T 0.552377 LowFisherScore;HighVafNormal;HighAltCntNormal SHARED;FETS=0.552377;TYPE=snv;LEN=1;KMERSIZE=15;SB=9.92656;SOURCES=mutect2,lancet GT:AD:SR:SA:DP 0/1:59,434:55,4:383,51:493
chr4 55161391 . T C 0 LowFisherScore;HighVafNormal;HighAltCntNormal SHARED;FETS=0;TYPE=snv;LEN=1;KMERSIZE=15;SB=0;SOURCES=mutect2,lancet GT:AD:SR:SA:DP 1/1:0,1263:0,0:547,716:1263
chr4 55161452 . A AG 0 LowFisherScore SOMATIC;FETS=0;TYPE=ins;LEN=1;KMERSIZE=15;SB=9.29406;SOURCES=lancet GT:AD:SR:SA:DP 0/1:932,67:221,711:16,51:999
chr4 55161483 . G A 0 LowFisherScore;LowVafTumor;LowAltCntTumor;StrandBias SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=13;SB=1.30227;SOURCES=lancet GT:AD:SR:SA:DP 0/1:688,2:96,592:0,2:690
chr4 55161517 . A G 0 LowFisherScore SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=13;SB=0;SOURCES=lancet GT:AD:SR:SA:DP 1/1:0,498:0,0:5,493:498
chr4 55161534 . C T 0 LowFisherScore;LowVafTumor;LowAltCntTumor;StrandBias SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=13;SB=0.110827;SOURCES=lancet GT:AD:SR:SA:DP 0/1:314,2:4,310:0,2:316
chr4 55524121 . G A . PASS AS_SB_TABLE=447,64|33,4;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=571;AS_FilterStatus=SITE;MBQ=38,38;MFRL=205,189;MMQ=60,60;MPOS=21;POPAF=4.61;TLOD=91.24 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:511,37:0.069:548:237,18:254,16:447,64,33,4
chr4 55524304 . T C . germline AS_SB_TABLE=130,303|113,390;ECNT=2;GERMQ=1;SOURCES=mutect2;DP=1067;AS_FilterStatus=SITE;MBQ=38,38;MFRL=162,167;MMQ=60,60;MPOS=20;POPAF=0.239;TLOD=1711.56 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:433,503:0.542:936:200,236:181,200:130,303,113,390
chr4 55524338 . A G . PASS AS_SB_TABLE=77,559|5,32;ECNT=2;GERMQ=93;SOURCES=mutect2;DP=703;AS_FilterStatus=SITE;MBQ=38,38;MFRL=188,178;MMQ=60,60;MPOS=19;POPAF=1.52;TLOD=90.3 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:636,37:0.058:673:271,12:215,18:77,559,5,32
chr4 55561862 . G T . PASS AS_SB_TABLE=493,683|49,55;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=1324;AS_FilterStatus=SITE;MBQ=38,38;MFRL=195,190;MMQ=60,60;MPOS=22;POPAF=1.82;TLOD=277.85 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:1176,104:0.083:1280:632,57:456,42:493,683,49,55
chr4 55575642 . T C . PASS AS_SB_TABLE=415,495|22,37;ECNT=2;GERMQ=93;SOURCES=mutect2;DP=1013;AS_FilterStatus=SITE;MBQ=38,37;MFRL=184,182;MMQ=60,60;MPOS=11;POPAF=7.3;TLOD=133.63 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:910,59:0.061:969:487,26:321,26:415,495,22,37
chr4 55575673 . A G . PASS AS_SB_TABLE=292,440|19,30;ECNT=2;GERMQ=93;SOURCES=mutect2;DP=824;AS_FilterStatus=SITE;MBQ=38,38;MFRL=180,181;MMQ=60,60;MPOS=20;POPAF=2.78;TLOD=124.78 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:732,49:0.065:781:349,28:249,14:292,440,19,30
chr4 55597458 . A G . PASS AS_SB_TABLE=858,318|64,20;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=1321;AS_FilterStatus=SITE;MBQ=38,38;MFRL=177,173;MMQ=60,60;MPOS=18;POPAF=1.72;TLOD=203.36 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:1176,84:0.067:1260:627,46:440,30:858,318,64,20
chr4 55598211 MantaDEL:166:0:0:0:1:0 ATTTTTTTTTTT A . . END=55598222;SVTYPE=DEL;SVLEN=-11;CIPOS=0,14;HOMLEN=14;HOMSEQ=TTTTTTTTTTTTTT;UPSTREAM_PAIR_COUNT=0;DOWNSTREAM_PAIR_COUNT=0;PAIR_COUNT=0;CIGAR=1M11D . .
chr4 55599321 . A T . PASS AS_SB_TABLE=252,324|17,32;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=644;AS_FilterStatus=SITE;MBQ=38,38;MFRL=180,174;MMQ=60,60;MPOS=22;POPAF=7.3;TLOD=121.84 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:576,49:0.077:625:298,27:219,12:252,324,17,32
chr4 55602765 . G C . PASS AS_SB_TABLE=783,631|42,30;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=1530;AS_FilterStatus=SITE;MBQ=38,38;MFRL=197,217;MMQ=60,60;MPOS=22;POPAF=0.839;TLOD=174.39 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:1414,72:0.05:1486:730,44:610,25:783,631,42,30
chr4 55604693 . C A . PASS AS_SB_TABLE=320,448|121,170;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=1082;AS_FilterStatus=SITE;MBQ=38,38;MFRL=158,165;MMQ=60,60;MPOS=20;POPAF=7.3;TLOD=874.27 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:768,291:0.284:1059:388,150:266,113:320,448,121,170
chr4 103583708 MantaDEL:179:0:0:0:2:0 CAAAAAAAAA C . . END=103583717;SVTYPE=DEL;SVLEN=-9;CIPOS=0,12;HOMLEN=12;HOMSEQ=AAAAAAAAAAAA;UPSTREAM_PAIR_COUNT=0;DOWNSTREAM_PAIR_COUNT=0;PAIR_COUNT=0;CIGAR=1M9D . .
chr5 1253744 . G A . PASS AS_SB_TABLE=87,3|292,16;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=441;AS_FilterStatus=SITE;MBQ=38,38;MFRL=219,200;MMQ=60,60;MPOS=19;POPAF=0.745;TLOD=1184.38 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:90,308:0.775:398:52,163:35,138:87,3,292,16
chr5 1254594 . C T . PASS AS_SB_TABLE=220,580|108,275;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=1258;AS_FilterStatus=SITE;MBQ=38,38;MFRL=170,173;MMQ=60,60;MPOS=18;POPAF=1.85;TLOD=1205.52 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:800,383:0.323:1183:392,174:308,166:220,580,108,275
chr5 1260509 . ACG A 0 LowFisherScore;LowVafTumor SOMATIC;FETS=0;TYPE=del;LEN=2;KMERSIZE=23;SB=9.91646;SOURCES=lancet GT:AD:SR:SA:DP 0/1:694,26:567,127:19,7:720
chr5 1260513 . G A 0 LowFisherSTR;LowVafTumor;StrandBias SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=25;SB=3.6026;MS=20CA;SOURCES=mutect2 GT:AD:SR:SA:DP 0/1:867,5:734,133:5,0:872
chr5 1260515 . G A 0 LowFisherSTR SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=23;SB=25.1192;MS=18CA;SOURCES GT:AD:SR:SA:DP 0/1:618,330:517,101:254,76:948
chr5 1260725 . AG A 0 LowFisherScore SOMATIC;FETS=0;TYPE=del;LEN=1;KMERSIZE=17;SB=10.2734;SOURCES=lancet GT:AD:SR:SA:DP 0/1:998,72:370,628:25,47:1070
chr5 1260755 . C T 0 LowFisherScore;LowVafTumor;StrandBias SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=17;SB=5.33976;SOURCES=lancet GT:AD:SR:SA:DP 0/1:914,3:308,606:0,3:917
chr5 1268847 . A C . PASS AS_SB_TABLE=51,524|5,53;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=660;AS_FilterStatus=SITE;MBQ=38,38;MFRL=176,200;MMQ=60,60;MPOS=18;POPAF=1.36;TLOD=148.67 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:575,58:0.092:633:276,23:243,29:51,524,5,53
chr5 1272498 . C T . PASS AS_SB_TABLE=93,672|6,45;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=866;AS_FilterStatus=SITE;MBQ=38,38;MFRL=198,213;MMQ=60,60;MPOS=19;POPAF=2.05;TLOD=121.95 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:765,51:0.063:816:370,30:337,18:93,672,6,45
chr5 1280429 . C T . PASS AS_SB_TABLE=347,665|37,81;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=1205;AS_FilterStatus=SITE;MBQ=38,38;MFRL=176,185;MMQ=60,60;MPOS=15;POPAF=7.3;TLOD=323.34 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:1012,118:0.108:1130:524,63:405,50:347,665,37,81
chr5 1293551 . C T . PASS AS_SB_TABLE=467,653|52,63;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=1313;AS_FilterStatus=SITE;MBQ=38,38;MFRL=182,175;MMQ=60,60;MPOS=17;POPAF=7.3;TLOD=298.7 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:1120,115:0.092:1235:589,61:418,40:467,653,52,63
chr5 1294089 . G A . PASS AS_SB_TABLE=693,758|77,102;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=1695;AS_FilterStatus=SITE;MBQ=38,38;MFRL=175,180;MMQ=60,60;MPOS=19;POPAF=7.3;TLOD=481.87 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:1451,179:0.112:1630:725,72:583,89:693,758,77,102
chr5 1294664 . CG C 0 LowFisherScore SOMATIC;FETS=0;TYPE=del;LEN=1;KMERSIZE=15;SB=36.8733;SOURCES=lancet GT:AD:SR:SA:DP 0/1:427,151:247,180:111,40:578
chr5 1294834 . TC T 0 LowFisherScore SOMATIC;FETS=0;TYPE=del;LEN=1;KMERSIZE=15;SB=22.364;SOURCES=lancet GT:AD:SR:SA:DP 0/1:329,132:53,276:10,122:461
chr5 1294858 . G A 0 LowFisherScore;LowVafTumor;LowAltCntTumor;StrandBias SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=19;SB=1.04561;SOURCES=lancet GT:AD:SR:SA:DP 0/1:360,2:41,319:0,2:362
chr5 1294933 . C T 0 LowFisherScore;LowVafTumor;LowAltCntTumor;StrandBias SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=19;SB=9.73846;SOURCES=lancet GT:AD:SR:SA:DP 0/1:178,2:57,121:2,0:180
chr5 1295183 . G A 0 LowFisherScore;LowVafTumor;StrandBias SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=19;SB=1.0789;SOURCES=lancet GT:AD:SR:SA:DP 0/1:149,3:12,137:0,3:152
chr5 61345614 MantaBND:197:0:1:0:0:0:1 A [chr6:117645154[A . . SVTYPE=BND;MATEID=MantaBND:197:0:1:0:0:0:0;CIPOS=0,12;HOMLEN=12;HOMSEQ=AAAGAAAAATAG;BND_PAIR_COUNT=1;PAIR_COUNT=1 . .
chr5 112043384 . T G . PASS AS_SB_TABLE=643,579|43,40;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=1377;AS_FilterStatus=SITE;MBQ=38,38;MFRL=151,157;MMQ=60,60;MPOS=18;POPAF=1;TLOD=187.65 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:1222,83:0.062:1305:483,32:578,37:643,579,43,40
chr5 112043492 . C A . PASS AS_SB_TABLE=414,476|21,31;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=984;AS_FilterStatus=SITE;MBQ=38,38;MFRL=181,176;MMQ=60,60;MPOS=23;POPAF=2.14;TLOD=121.71 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:890,52:0.056:942:397,19:403,27:414,476,21,31
chr5 112090586 . G T . PASS AS_SB_TABLE=290,145|35,12;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=517;AS_FilterStatus=SITE;MBQ=38,38;MFRL=197,193;MMQ=60,60;MPOS=20;POPAF=7.3;TLOD=116.66 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:435,47:0.094:482:248,26:168,16:290,145,35,12
chr5 112111508 . A G 0 LowFisherScore;StrandBias SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=15;SB=0;SOURCES=mutect2,lancet GT:AD:SR:SA:DP 0/1:67,3:0,67:0,3:70
chr5 112116632 . C T . PASS AS_SB_TABLE=12,231|1,18;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=266;AS_FilterStatus=SITE;MBQ=38,38;MFRL=223,263;MMQ=60,60;MPOS=15;POPAF=1.14;TLOD=48.41 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:243,19:0.076:262:151,8:89,11:12,231,1,18
chr5 112128308 . A G . PASS AS_SB_TABLE=1,76|0,6;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=85;AS_FilterStatus=SITE;MBQ=38,38;MFRL=207,176;MMQ=60,60;MPOS=20;POPAF=7.3;TLOD=15.06 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:77,6:0.082:83:51,5:26,1:1,76,0,6
chr5 112154571 . G C . PASS AS_SB_TABLE=398,0|39,0;ECNT=2;GERMQ=93;SOURCES=mutect2;DP=449;AS_FilterStatus=SITE;MBQ=37,37;MFRL=232,249;MMQ=60,60;MPOS=16;POPAF=1.02;TLOD=87.14 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:398,39:0.087:437:207,24:171,12:398,0,39,0
chr5 112154629 . C T . PASS AS_SB_TABLE=753,173|72,7;ECNT=2;GERMQ=93;SOURCES=mutect2;DP=1061;AS_FilterStatus=SITE;MBQ=38,38;MFRL=191,195;MMQ=60,60;MPOS=23;POPAF=7.3;TLOD=203.92 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:926,79:0.082:1005:457,36:336,40:753,173,72,7
chr5 112155046 . G A . PASS AS_SB_TABLE=196,568|4,21;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=837;AS_FilterStatus=SITE;MBQ=38,38;MFRL=188,207;MMQ=60,60;MPOS=17;POPAF=7.3;TLOD=56.81 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:764,25:0.035:789:431,10:264,15:196,568,4,21
chr5 112162700 . T C 0 LowFisherScore;LowVafTumor;LowAltCntTumor;StrandBias SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=19;SB=0;SOURCES=lancet GT:AD:SR:SA:DP 0/1:337,2:337,0:2,0:339
chr5 112162804 . G A 0 LowFisherScore;LowVafTumor SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=19;SB=3.70807;SOURCES=lancet GT:AD:SR:SA:DP 0/1:824,3:480,344:2,1:827
chr5 112162811 . T C 0 LowFisherScore;LowVafTumor;StrandBias SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=19;SB=7.47206;SOURCES=lancet GT:AD:SR:SA:DP 0/1:832,3:468,364:3,0:835
chr5 112162854 . T C 4.28147 LowFisherScore;HighVafNormal;HighAltCntNormal SHARED;FETS=4.28147;TYPE=snv;LEN=1;KMERSIZE=15;SB=15.5425;SOURCES=mutect2,lancet GT:AD:SR:SA:DP 0/1:655,215:263,392:97,118:870
chr5 112164561 . G A . PASS AS_SB_TABLE=116,34|39,9;ECNT=1;GERMQ=71;SOURCES=mutect2;DP=227;AS_FilterStatus=SITE;MBQ=38,38;MFRL=209,221;MMQ=60,60;MPOS=22;POPAF=0.225;TLOD=148.15 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:150,48:0.249:198:87,24:57,22:116,34,39,9
chr5 112175651 . A G . PASS AS_SB_TABLE=701,604|54,43;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=1470;AS_FilterStatus=SITE;MBQ=38,38;MFRL=211,200;MMQ=60,60;MPOS=15;POPAF=2.65;TLOD=242.29 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:1305,97:0.069:1402:584,53:638,35:701,604,54,43
chr5 112175770 . G A . PASS AS_SB_TABLE=466,520|196,248;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=1533;AS_FilterStatus=SITE;MBQ=38,38;MFRL=200,209;MMQ=60,60;MPOS=17;POPAF=0.225;TLOD=1427.8 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:986,444:0.317:1430:457,220:428,188:466,520,196,248
chr5 112176184 . T C . PASS AS_SB_TABLE=763,772|54,57;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=1687;AS_FilterStatus=SITE;MBQ=38,38;MFRL=192,194;MMQ=60,60;MPOS=17;POPAF=2.65;TLOD=259.92 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:1535,111:0.065:1646:768,58:636,40:763,772,54,57
chr5 112176325 . G A . PASS AS_SB_TABLE=495,525|219,240;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=1529;AS_FilterStatus=SITE;MBQ=38,38;MFRL=213,229;MMQ=60,60;MPOS=19;POPAF=0.223;TLOD=1486.4 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:1020,459:0.315:1479:548,245:408,197:495,525,219,240
chr5 112176559 . T G . PASS AS_SB_TABLE=204,463|54,193;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=981;AS_FilterStatus=SITE;MBQ=38,38;MFRL=210,245;MMQ=60,60;MPOS=19;POPAF=0.224;TLOD=785.57 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:667,247:0.277:914:368,169:241,65:204,463,54,193
chr5 112176756 . T A . PASS AS_SB_TABLE=176,184|90,73;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=583;AS_FilterStatus=SITE;MBQ=38,38;MFRL=306,272;MMQ=60,60;MPOS=14;POPAF=0.096;TLOD=528.15 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:360,163:0.311:523:198,104:156,55:176,184,90,73
chr5 112177171 . G A . PASS AS_SB_TABLE=294,352|177,196;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=1131;AS_FilterStatus=SITE;MBQ=38,38;MFRL=225,246;MMQ=60,60;MPOS=18;POPAF=0.224;TLOD=1234.44 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:646,373:0.367:1019:317,201:299,155:294,352,177,196
chr5 112179344 . A G . PASS AS_SB_TABLE=763,389|52,41;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=1329;AS_FilterStatus=SITE;MBQ=38,38;MFRL=221,220;MMQ=60,60;MPOS=19;POPAF=7.3;TLOD=241.44 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:1152,93:0.076:1245:571,42:545,50:763,389,52,41
chr5 112179431 . C T . PASS AS_SB_TABLE=398,472|149,195;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=1254;AS_FilterStatus=SITE;MBQ=38,38;MFRL=199,205;MMQ=60,60;MPOS=18;POPAF=7.3;TLOD=1109 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:870,344:0.288:1214:463,176:360,157:398,472,149,195
chr5 155951763 MantaBND:113:1:2:0:0:0:1 T [chr3:41275569[T . . SVTYPE=BND;MATEID=MantaBND:113:1:2:0:0:0:0;CIPOS=0,7;HOMLEN=7;HOMSEQ=CCCACCC;BND_PAIR_COUNT=1;PAIR_COUNT=1 . .
chr6 54635604 MantaDEL:222:0:0:0:0:0 GCGGGGGGGG GGC . . END=54635613;SVTYPE=DEL;SVLEN=-9;UPSTREAM_PAIR_COUNT=0;DOWNSTREAM_PAIR_COUNT=0;PAIR_COUNT=0;CIGAR=1M2I9D . .
chr6 117639262 . G A . PASS AS_SB_TABLE=381,5|50,1;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=441;AS_FilterStatus=SITE;MBQ=38,38;MFRL=213,235;MMQ=60,60;MPOS=21;POPAF=1.33;TLOD=138.31 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:386,51:0.116:437:233,15:150,34:381,5,50,1
chr6 117641952 . T A . PASS AS_SB_TABLE=588,275|191,102;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=1201;AS_FilterStatus=SITE;MBQ=38,38;MFRL=228,229;MMQ=60,60;MPOS=18;POPAF=7.3;TLOD=938.75 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:863,293:0.255:1156:471,163:364,123:588,275,191,102
chr6 117642618 . A T 0 LowFisherScore;LowVafTumor;StrandBias SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=23;SB=0.0627898;SOURCES=lancet GT:AD:SR:SA:DP 0/1:622,3:3,619:0,3:625
chr6 117642992 MantaDEL:244:0:0:0:4:0 ATTTTTTTT A . . END=117643000;SVTYPE=DEL;SVLEN=-8;CIPOS=0,12;HOMLEN=12;HOMSEQ=TTTTTTTTTTTT;UPSTREAM_PAIR_COUNT=0;DOWNSTREAM_PAIR_COUNT=0;PAIR_COUNT=0;CIGAR=1M8D . .
chr6 117643188 . AT A 0 LowFisherScore SOMATIC;FETS=0;TYPE=del;LEN=1;KMERSIZE=23;SB=6.54055;SOURCES=lancet GT:AD:SR:SA:DP 0/1:56,7:30,26:5,2:63
chr6 117643588 . A G 0 LowFisherScore SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=15;SB=13.4582;SOURCES=mutect2,lancet GT:AD:SR:SA:DP 0/1:806,366:435,371:203,163:1172
chr6 117645142 MantaBND:197:0:1:0:0:0:0 T [chr5:61345626[T . . SVTYPE=BND;MATEID=MantaBND:197:0:1:0:0:0:1;CIPOS=0,12;HOMLEN=12;HOMSEQ=ATTTTTCTTTTA;BND_PAIR_COUNT=1;PAIR_COUNT=1 . .
chr6 117645352 . A G 0 LowFisherScore SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=13;SB=8.96082;SOURCES=mutect2,lancet GT:AD:SR:SA:DP 0/1:483,37:283,200:23,14:520
chr6 117645652 . C T 0 LowFisherScore SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=13;SB=8.997;SOURCES=mutect2,lancet GT:AD:SR:SA:DP 0/1:528,44:316,212:26,18:572
chr6 117645662 . T C 0 LowFisherScore SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=13;SB=9.7354;SOURCES=mutect2,lancet GT:AD:SR:SA:DP 0/1:480,43:268,212:22,21:523
chr6 117646759 . C T 0 LowFisherScore SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=37;SB=11.8994;SOURCES=mutect2,lancet GT:AD:SR:SA:DP 0/1:191,78:68,123:33,45:269
chr6 117647254 MantaDEL:240:0:0:0:1:0 TTATATATATA T . . END=117647264;SVTYPE=DEL;SVLEN=-10;CIPOS=0,26;HOMLEN=26;HOMSEQ=TATATATATATATATATATATATATA;UPSTREAM_PAIR_COUNT=0;DOWNSTREAM_PAIR_COUNT=0;PAIR_COUNT=0;CIGAR=1M10D . .
chr6 117647915 . T C . PASS AS_SB_TABLE=420,330|45,32;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=916;AS_FilterStatus=SITE;MBQ=38,38;MFRL=264,272;MMQ=60,60;MPOS=20;POPAF=2.31;TLOD=206.55 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:750,77:0.094:827:441,43:297,33:420,330,45,32
chr6 117650965 . C T . PASS AS_SB_TABLE=680,522|51,52;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=1344;AS_FilterStatus=SITE;MBQ=38,38;MFRL=175,164;MMQ=60,60;MPOS=24;POPAF=7.3;TLOD=257.06 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:1202,103:0.08:1305:595,63:471,30:680,522,51,52
chr6 117651947 . A G . clustered_events;haplotype AS_SB_TABLE=106,120|16,10;ECNT=4;GERMQ=93;SOURCES=mutect2;DP=268;AS_FilterStatus=SITE;MBQ=38,38;MFRL=246,262;MMQ=60,60;MPOS=14;POPAF=2.59;TLOD=77.7 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:226,26:0.109:252:105,11:92,15:0|1:117651947_A_G:117651947:106,120,16,10
chr6 117651957 . T A . clustered_events;haplotype AS_SB_TABLE=122,114|16,8;ECNT=4;GERMQ=93;SOURCES=mutect2;DP=266;AS_FilterStatus=SITE;MBQ=38,38;MFRL=250,272;MMQ=60,60;MPOS=11;POPAF=7.3;TLOD=70.39 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:236,24:0.097:260:116,12:104,11:0|1:117651947_A_G:117651947:122,114,16,8
chr6 117651960 . A T . clustered_events AS_SB_TABLE=138,114|3,1;ECNT=4;GERMQ=93;SOURCES=mutect2;DP=269;AS_FilterStatus=SITE;MBQ=38,29;MFRL=255,157;MMQ=60,60;MPOS=17;POPAF=3.71;TLOD=4.63 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:252,4:0.016:256:126,1:114,2:138,114,3,1
chr6 117652033 . T C . base_qual;clustered_events;strand_bias AS_SB_TABLE=167,68|26,0;ECNT=4;GERMQ=93;SOURCES=mutect2;DP=281;AS_FilterStatus=base_qual;MBQ=32,12;MFRL=229,217;MMQ=60,60;MPOS=20;POPAF=7.3;TLOD=13.19 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:235,26:0.068:261:94,5:88,6:167,68,26,0
chr6 117654711 . T C . germline AS_SB_TABLE=0,0|1,6;ECNT=1;GERMQ=1;SOURCES=mutect2;DP=7;AS_FilterStatus=SITE;MBQ=0,38;MFRL=0,216;MMQ=60,60;MPOS=14;POPAF=0.0008695;TLOD=28.1 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:0,7:0.889:7:0,2:0,5:0,0,1,6
chr6 117656555 . T G . germline AS_SB_TABLE=17,17|14,8;ECNT=1;GERMQ=1;SOURCES=mutect2;DP=56;AS_FilterStatus=SITE;MBQ=38,38;MFRL=246,244;MMQ=60,60;MPOS=19;POPAF=0.112;TLOD=74.55 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:34,22:0.397:56:17,13:17,9:17,17,14,8
chr6 117656893 . A G . PASS AS_SB_TABLE=53,20|2,1;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=79;AS_FilterStatus=SITE;MBQ=38,38;MFRL=145,125;MMQ=60,60;MPOS=15;POPAF=7.3;TLOD=4 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:73,3:0.054:76:43,1:21,1:53,20,2,1
chr6 117657493 . T C . clustered_events;strand_bias AS_SB_TABLE=54,170|10,0;ECNT=3;GERMQ=93;SOURCES=mutect2;DP=252;AS_FilterStatus=strand_bias;MBQ=38,22;MFRL=245,239;MMQ=60,60;MPOS=28;POPAF=7.3;TLOD=12.62 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:224,10:0.036:234:94,5:78,1:54,170,10,0
chr6 117657510 . A C . clustered_events;strand_bias AS_SB_TABLE=70,108|15,0;ECNT=3;GERMQ=93;SOURCES=mutect2;DP=204;AS_FilterStatus=strand_bias;MBQ=38,22;MFRL=273,353;MMQ=60,60;MPOS=11;POPAF=7.3;TLOD=16.98 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:178,15:0.066:193:79,5:73,3:70,108,15,0
chr6 117657523 . C T . base_qual;clustered_events;strand_bias AS_SB_TABLE=92,79|12,0;ECNT=3;GERMQ=93;SOURCES=mutect2;DP=192;AS_FilterStatus=base_qual;MBQ=38,11;MFRL=276,308;MMQ=60,60;MPOS=9;POPAF=7.3;TLOD=34.01 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:171,12:0.075:183:74,1:78,2:92,79,12,0
chr6 117657651 . CA C 0 LowFisherScore SOMATIC;FETS=0;TYPE=del;LEN=1;KMERSIZE=13;SB=7.30334;SOURCES=lancet GT:AD:SR:SA:DP 0/1:474,36:399,75:31,5:510
chr6 117660919 . G A . PASS AS_SB_TABLE=333,416|151,210;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=1158;AS_FilterStatus=SITE;MBQ=38,38;MFRL=214,210;MMQ=60,60;MPOS=19;POPAF=7.3;TLOD=1178.16 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:749,361:0.325:1110:395,196:330,155:333,416,151,210
chr6 117661264 . T C . PASS AS_SB_TABLE=181,284|92,137;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=747;AS_FilterStatus=SITE;MBQ=38,38;MFRL=252,263;MMQ=60,60;MPOS=17;POPAF=0.05;TLOD=762.54 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:465,229:0.33:694:269,128:185,96:181,284,92,137
chr6 117661776 . G T 0 LowFisherScore SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=17;SB=13.0799;SOURCES=mutect2,lancet GT:AD:SR:SA:DP 0/1:390,37:329,61:35,2:427
chr6 117663212 . GA G 0 LowFisherScore SOMATIC;FETS=0;TYPE=del;LEN=1;KMERSIZE=15;SB=8.1084;SOURCES=lancet GT:AD:SR:SA:DP 0/1:540,38:69,471:3,35:578
chr6 117663310 . C T 0 LowFisherScore;LowVafTumor;LowAltCntTumor;StrandBias SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=19;SB=1.04151;SOURCES=lancet GT:AD:SR:SA:DP 0/1:87,2:10,77:0,2:89
chr6 117663588 . C T 0 LowFisherScore;LowVafTumor;LowAltCntTumor SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=19;SB=3.29663;SOURCES=lancet GT:AD:SR:SA:DP 0/1:351,2:221,130:1,1:353
chr6 117674205 MantaBND:149:0:1:0:0:0:0 G G[chr4:27964519[ . . SVTYPE=BND;MATEID=MantaBND:149:0:1:0:0:0:1;CIPOS=0,5;HOMLEN=5;HOMSEQ=GCCTT;BND_PAIR_COUNT=1;PAIR_COUNT=1 . .
chr6 117678083 . A G . germline AS_SB_TABLE=15,214|27,230;ECNT=1;GERMQ=1;SOURCES=mutect2;DP=561;AS_FilterStatus=SITE;MBQ=38,38;MFRL=227,229;MMQ=60,60;MPOS=19;POPAF=0.377;TLOD=900.26 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:229,257:0.524:486:126,153:96,95:15,214,27,230
chr6 117681577 . A G 0 LowFisherScore;LowVafTumor;LowAltCntTumor;StrandBias SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=15;SB=5.32916;SOURCES=lancet GT:AD:SR:SA:DP 0/1:439,2:202,237:0,2:441
chr6 117686448 . A G 0 LowFisherScore;StrandBias SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=13;SB=0.677051;SOURCES=lancet GT:AD:SR:SA:DP 0/1:76,4:3,73:0,4:80
chr6 117686840 . T C 0 LowFisherScore SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=13;SB=15.8188;SOURCES=mutect2,lancet GT:AD:SR:SA:DP 0/1:212,154:31,181:13,141:366
chr6 117686943 . A T 0 LowFisherScore SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=13;SB=8.27689;SOURCES=mutect2,lancet GT:AD:SR:SA:DP 0/1:82,92:10,72:14,78:174
chr6 117714346 . C G . germline AS_SB_TABLE=268,41|219,34;ECNT=1;GERMQ=1;SOURCES=mutect2;DP=605;AS_FilterStatus=SITE;MBQ=38,38;MFRL=177,185;MMQ=60,60;MPOS=24;POPAF=0.315;TLOD=848.63 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:309,253:0.447:562:162,125:128,112:268,41,219,34
chr6 117715756 . T C . PASS AS_SB_TABLE=220,18|7,0;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=261;AS_FilterStatus=SITE;MBQ=38,38;MFRL=199,173;MMQ=60,60;MPOS=8;POPAF=7.3;TLOD=14.71 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:238,7:0.034:245:124,1:98,6:220,18,7,0
chr6 117718110 . C T . PASS AS_SB_TABLE=397,137|212,48;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=851;AS_FilterStatus=SITE;MBQ=38,38;MFRL=189,192;MMQ=60,60;MPOS=21;POPAF=7.3;TLOD=853.78 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:534,260:0.329:794:285,130:216,111:397,137,212,48
chr6 117724428 . G A . PASS AS_SB_TABLE=249,634|33,77;ECNT=2;GERMQ=93;SOURCES=mutect2;DP=1034;AS_FilterStatus=SITE;MBQ=38,38;MFRL=166,171;MMQ=60,60;MPOS=22;POPAF=7.3;TLOD=287.23 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:883,110:0.111:993:451,56:297,38:249,634,33,77
chr6 117724462 . C A . germline AS_SB_TABLE=39,339|42,306;ECNT=2;GERMQ=1;SOURCES=mutect2;DP=761;AS_FilterStatus=SITE;MBQ=38,38;MFRL=180,187;MMQ=60,60;MPOS=18;POPAF=0.22;TLOD=1195.39 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:378,348:0.48:726:172,162:94,102:39,339,42,306
chr6 117725578 . T A . germline AS_SB_TABLE=156,296|121,258;ECNT=1;GERMQ=1;SOURCES=mutect2;DP=894;AS_FilterStatus=SITE;MBQ=38,38;MFRL=166,171;MMQ=60,60;MPOS=23;POPAF=0.218;TLOD=1244.5 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:452,379:0.46:831:247,189:141,140:156,296,121,258
chr6 117730819 . G A . germline AS_SB_TABLE=285,300|219,319;ECNT=1;GERMQ=1;SOURCES=mutect2;DP=1179;AS_FilterStatus=SITE;MBQ=38,38;MFRL=160,166;MMQ=60,60;MPOS=17;POPAF=0.507;TLOD=1753.81 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:585,538:0.481:1123:272,258:239,212:285,300,219,319
chr6 117735450 . A C 0 LowFisherScore;StrandBias SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=17;SB=0;SOURCES=lancet GT:AD:SR:SA:DP 0/1:25,20:25,0:20,0:45
chr6 117735569 . G A 0.0407791 LowFisherScore;LowVafTumor;LowAltCntTumor;StrandBias SOMATIC;FETS=0.0407791;TYPE=snv;LEN=1;KMERSIZE=17;SB=0;SOURCES=lancet GT:AD:SR:SA:DP 0/1:211,2:211,0:2,0:213
chr6 117735603 . C T 0.0265624 LowFisherScore;LowVafTumor;LowAltCntTumor;StrandBias SOMATIC;FETS=0.0265624;TYPE=snv;LEN=1;KMERSIZE=17;SB=0.215475;SOURCES=lancet GT:AD:SR:SA:DP 0/1:325,2:317,8:2,0:327
chr6 117737390 . G A . germline AS_SB_TABLE=89,11|77,6;ECNT=1;GERMQ=1;SOURCES=mutect2;DP=204;AS_FilterStatus=SITE;MBQ=38,38;MFRL=208,227;MMQ=60,60;MPOS=19;POPAF=0.431;TLOD=286 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:100,83:0.456:183:52,47:47,35:89,11,77,6
chr6 151397367 MantaINS:253:0:0:0:0:0 G GCCTGTAGT . . END=151397367;SVTYPE=INS;SVLEN=8;CIPOS=0,3;HOMLEN=3;HOMSEQ=CCT;UPSTREAM_PAIR_COUNT=0;DOWNSTREAM_PAIR_COUNT=0;PAIR_COUNT=0;CIGAR=1M8I . .
chr7 54889362 . T G . PASS AS_SB_TABLE=30,2|177,7;ECNT=2;GERMQ=93;SOURCES=mutect2;DP=236;AS_FilterStatus=SITE;MBQ=38,38;MFRL=200,201;MMQ=60,60;MPOS=20;POPAF=0.327;TLOD=699.9 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:32,184:0.845:216:16,96:14,79:30,2,177,7
chr7 54889414 . T C . PASS AS_SB_TABLE=58,14|257,47;ECNT=2;GERMQ=93;SOURCES=mutect2;DP=390;AS_FilterStatus=SITE;MBQ=38,38;MFRL=178,167;MMQ=60,60;MPOS=23;POPAF=0.491;TLOD=1151.95 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:72,304:0.803:376:34,160:26,106:58,14,257,47
chr7 54905292 . A G . PASS AS_SB_TABLE=170,7|14,0;ECNT=2;GERMQ=93;SOURCES=mutect2;DP=204;AS_FilterStatus=SITE;MBQ=38,38;MFRL=236,250;MMQ=60,60;MPOS=15;POPAF=1.37;TLOD=34.93 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:177,14:0.078:191:105,9:69,5:170,7,14,0
chr7 54905350 . T C . PASS AS_SB_TABLE=48,22|152,57;ECNT=2;GERMQ=93;SOURCES=mutect2;DP=296;AS_FilterStatus=SITE;MBQ=38,38;MFRL=182,195;MMQ=60,60;MPOS=16;POPAF=0.602;TLOD=782.84 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:70,209:0.745:279:39,110:17,67:48,22,152,57
chr7 54912662 . C T . PASS AS_SB_TABLE=44,13|179,43;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=297;AS_FilterStatus=SITE;MBQ=38,38;MFRL=189,199;MMQ=60,60;MPOS=18;POPAF=0.345;TLOD=846.93 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:57,222:0.796:279:29,132:25,81:44,13,179,43
chr7 54926166 . A G . PASS AS_SB_TABLE=480,380|51,44;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=1008;AS_FilterStatus=SITE;MBQ=38,38;MFRL=154,163;MMQ=60,60;MPOS=21;POPAF=0.296;TLOD=245.73 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:860,95:0.103:955:378,43:369,43:480,380,51,44
chr7 54934751 . C T 0 LowFisherScore;LowVafTumor;LowAltCntTumor;StrandBias SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=15;SB=4.98988;SOURCES=lancet GT:AD:SR:SA:DP 0/1:312,2:175,137:2,0:314
chr7 54934795 . AG A 0 LowFisherScore SOMATIC;FETS=0;TYPE=del;LEN=1;KMERSIZE=15;SB=14.0059;SOURCES=lancet GT:AD:SR:SA:DP 0/1:424,39:240,184:17,22:463
chr7 54934812 . T C 0 LowFisherScore SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=15;SB=19.0586;SOURCES=mutect2,lancet GT:AD:SR:SA:DP 0/1:400,60:218,182:24,36:460
chr7 54934814 . A G 0 LowFisherScore SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=15;SB=9.53023;SOURCES=mutect2,lancet GT:AD:SR:SA:DP 0/1:372,26:204,168:12,14:398
chr7 54934859 . T A 0 LowFisherScore;LowVafTumor;LowAltCntTumor;StrandBias SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=15;SB=2.64456;SOURCES=lancet GT:AD:SR:SA:DP 0/1:349,2:92,257:0,2:351
chr7 54934870 . C G 0 LowFisherScore SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=15;SB=7.95026;SOURCES=mutect2,lancet GT:AD:SR:SA:DP 0/1:292,32:65,227:8,24:324
chr7 54934872 . G A 0 LowFisherScore SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=15;SB=9.53276;SOURCES=mutect2,lancet GT:AD:SR:SA:DP 0/1:289,15:63,226:1,14:304
chr7 54950476 . C A . PASS AS_SB_TABLE=383,97|21,7;ECNT=2;GERMQ=93;SOURCES=mutect2;DP=556;AS_FilterStatus=SITE;MBQ=38,38;MFRL=194,191;MMQ=60,60;MPOS=20;POPAF=0.914;TLOD=55.64 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:480,28:0.054:508:252,19:179,7:383,97,21,7
chr7 54950551 . T C . PASS AS_SB_TABLE=560,284|33,14;ECNT=2;GERMQ=93;SOURCES=mutect2;DP=956;AS_FilterStatus=SITE;MBQ=38,38;MFRL=178,177;MMQ=60,60;MPOS=17;POPAF=0.455;TLOD=107.48 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:844,47:0.054:891:379,24:274,15:560,284,33,14
chr7 54961755 . T G . PASS AS_SB_TABLE=6,37|25,286;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=389;AS_FilterStatus=SITE;MBQ=38,38;MFRL=196,191;MMQ=60,60;MPOS=15;POPAF=0.341;TLOD=1198.99 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:43,311:0.874:354:26,154:16,133:6,37,25,286
chr7 54970059 . C A . PASS AS_SB_TABLE=13,71|62,400;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=591;AS_FilterStatus=SITE;MBQ=38,38;MFRL=182,176;MMQ=60,60;MPOS=17;POPAF=0.311;TLOD=1716.04 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:84,462:0.841:546:48,259:32,159:13,71,62,400
chr7 54970151 . C A . PASS AS_SB_TABLE=1,28|0,147;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=181;AS_FilterStatus=SITE;MBQ=38,38;MFRL=241,263;MMQ=60,60;MPOS=16;POPAF=0.533;TLOD=584.66 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:29,147:0.836:176:19,80:9,67:1,28,0,147
chr7 54983916 . T C . PASS AS_SB_TABLE=410,349|57,37;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=894;AS_FilterStatus=SITE;MBQ=38,38;MFRL=164,168;MMQ=60,60;MPOS=17;POPAF=0.391;TLOD=254.9 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:759,94:0.114:853:402,51:279,34:410,349,57,37
chr7 55028474 . C G . PASS AS_SB_TABLE=270,316|27,32;ECNT=2;GERMQ=93;SOURCES=mutect2;DP=663;AS_FilterStatus=SITE;MBQ=38,38;MFRL=177,168;MMQ=60,60;MPOS=18;POPAF=0.431;TLOD=154.83 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:586,59:0.093:645:307,29:244,27:270,316,27,32
chr7 55028539 . G A . PASS AS_SB_TABLE=205,380|10,11;ECNT=2;GERMQ=93;SOURCES=mutect2;DP=655;AS_FilterStatus=SITE;MBQ=38,38;MFRL=171,168;MMQ=60,60;MPOS=21;POPAF=1.24;TLOD=48.68 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:585,21:0.04:606:228,6:172,10:205,380,10,11
chr7 55040005 . A G . PASS AS_SB_TABLE=2,206|2,10;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=242;AS_FilterStatus=SITE;MBQ=38,38;MFRL=213,167;MMQ=60,60;MPOS=16;POPAF=2.12;TLOD=26.63 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:208,12:0.054:220:109,8:97,3:2,206,2,10
chr7 55046540 . T A . PASS AS_SB_TABLE=397,261|47,30;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=794;AS_FilterStatus=SITE;MBQ=38,38;MFRL=156,150;MMQ=60,60;MPOS=16;POPAF=0.391;TLOD=193.27 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:658,77:0.102:735:310,33:268,34:397,261,47,30
chr7 55058006 . T C . PASS AS_SB_TABLE=328,367|31,27;ECNT=2;GERMQ=93;SOURCES=mutect2;DP=772;AS_FilterStatus=SITE;MBQ=38,38;MFRL=155,155;MMQ=60,60;MPOS=20;POPAF=0.407;TLOD=151.95 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:695,58:0.084:753:311,33:287,23:328,367,31,27
chr7 55058033 . G A . PASS AS_SB_TABLE=274,450|9,17;ECNT=2;GERMQ=93;SOURCES=mutect2;DP=767;AS_FilterStatus=SITE;MBQ=38,38;MFRL=154,172;MMQ=60,60;MPOS=18;POPAF=1.29;TLOD=55.16 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:724,26:0.037:750:294,11:260,12:274,450,9,17
chr7 55065119 . A G . PASS AS_SB_TABLE=168,205|17,32;ECNT=2;GERMQ=93;SOURCES=mutect2;DP=449;AS_FilterStatus=SITE;MBQ=38,38;MFRL=175,189;MMQ=60,60;MPOS=17;POPAF=0.412;TLOD=135.56 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:373,49:0.119:422:192,23:155,21:168,205,17,32
chr7 55065175 . A G . PASS AS_SB_TABLE=36,319|2,13;ECNT=2;GERMQ=93;SOURCES=mutect2;DP=383;AS_FilterStatus=SITE;MBQ=38,38;MFRL=200,238;MMQ=60,60;MPOS=17;POPAF=1.38;TLOD=31.31 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:355,15:0.042:370:127,5:106,7:36,319,2,13
chr7 55083203 . A T 0 LowFisherScore;StrandBias SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=13;SB=0;SOURCES=lancet GT:AD:SR:SA:DP 0/1:123,7:123,0:7,0:130
chr7 55083281 . TG T 0 LowFisherScore SOMATIC;FETS=0;TYPE=del;LEN=1;KMERSIZE=13;SB=8.90504;SOURCES=lancet GT:AD:SR:SA:DP 0/1:57,165:42,15:126,39:222
chr7 55087139 . G T . PASS AS_SB_TABLE=10,291|1,20;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=334;AS_FilterStatus=SITE;MBQ=38,38;MFRL=206,183;MMQ=60,60;MPOS=26;POPAF=0.854;TLOD=51.49 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:301,21:0.065:322:169,10:126,10:10,291,1,20
chr7 55136385 . A G 0 LowFisherScore;LowVafTumor;LowAltCntTumor SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=21;SB=3.01364;SOURCES=lancet GT:AD:SR:SA:DP 0/1:519,2:246,273:1,1:521
chr7 55136397 . C T 0 LowFisherScore SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=21;SB=10.7129;SOURCES=mutect2,lancet GT:AD:SR:SA:DP 0/1:87,482:36,51:212,270:569
chr7 55208277 . G A . haplotype AS_SB_TABLE=39,39|202,194;ECNT=2;GERMQ=93;SOURCES=mutect2;DP=507;AS_FilterStatus=SITE;MBQ=38,38;MFRL=175,180;MMQ=60,60;MPOS=18;POPAF=0.364;TLOD=1517.07 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:78,396:0.833:474:45,235:27,138:0|1:55208277_G_A:55208277:39,39,202,194
chr7 55208284 . C A . germline;haplotype AS_SB_TABLE=0,0|245,237;ECNT=2;GERMQ=1;SOURCES=mutect2;DP=515;AS_FilterStatus=SITE;MBQ=0,38;MFRL=0,180;MMQ=60,60;MPOS=15;POPAF=0.06;TLOD=2117.46 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,482:0.998:482:0,269:0,156:0|1:55208277_G_A:55208277:0,0,245,237
chr7 55210975 . G A . PASS AS_SB_TABLE=653,148|219,55;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=1128;AS_FilterStatus=SITE;MBQ=38,38;MFRL=191,184;MMQ=60,60;MPOS=20;POPAF=7.3;TLOD=848.56 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:801,274:0.258:1075:393,133:347,120:653,148,219,55
chr7 55214348 . C T . PASS AS_SB_TABLE=242,130|808,518;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=1760;AS_FilterStatus=SITE;MBQ=38,38;MFRL=166,162;MMQ=60,60;MPOS=18;POPAF=0.298;TLOD=4767.46 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:372,1326:0.78:1698:193,672:141,500:242,130,808,518
chr7 55214443 . G A . PASS AS_SB_TABLE=540,900|47,74;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=1660;AS_FilterStatus=SITE;MBQ=38,38;MFRL=162,165;MMQ=60,60;MPOS=17;POPAF=1.17;TLOD=298.28 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:1440,121:0.076:1561:716,69:538,36:540,900,47,74
chr7 55218903 . T C . PASS AS_SB_TABLE=185,74|767,274;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=1366;AS_FilterStatus=SITE;MBQ=38,38;MFRL=203,196;MMQ=60,60;MPOS=16;POPAF=0.285;TLOD=3937.51 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:259,1041:0.796:1300:136,538:114,436:185,74,767,274
chr7 55219159 . C T . PASS AS_SB_TABLE=80,205|274,804;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=1440;AS_FilterStatus=SITE;MBQ=38,38;MFRL=185,192;MMQ=60,60;MPOS=16;POPAF=0.272;TLOD=4090.02 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:285,1078:0.789:1363:169,584:100,433:80,205,274,804
chr7 55220177 . A G . PASS AS_SB_TABLE=73,35|480,142;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=789;AS_FilterStatus=SITE;MBQ=38,38;MFRL=178,179;MMQ=60,60;MPOS=15;POPAF=0.238;TLOD=2350.1 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:108,622:0.853:730:51,330:46,240:73,35,480,142
chr7 55221655 . G A . PASS AS_SB_TABLE=908,105|86,7;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=1169;AS_FilterStatus=SITE;MBQ=38,38;MFRL=174,171;MMQ=60,60;MPOS=23;POPAF=0.602;TLOD=243.47 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:1013,93:0.086:1106:499,48:449,41:908,105,86,7
chr7 55228053 . A T . PASS AS_SB_TABLE=42,423|16,123;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=627;AS_FilterStatus=SITE;MBQ=38,38;MFRL=218,234;MMQ=60,60;MPOS=21;POPAF=0.158;TLOD=435.34 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:465,139:0.231:604:238,75:200,53:42,423,16,123
chr7 55232246 . T C . PASS AS_SB_TABLE=363,10|23,1;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=425;AS_FilterStatus=SITE;MBQ=38,38;MFRL=233,219;MMQ=60,60;MPOS=14;POPAF=0.602;TLOD=60.33 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:373,24:0.064:397:223,12:141,12:363,10,23,1
chr7 55232333 . A G . PASS AS_SB_TABLE=486,277|27,12;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=836;AS_FilterStatus=SITE;MBQ=38,38;MFRL=188,184;MMQ=60,60;MPOS=22;POPAF=0.629;TLOD=91.15 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:763,39:0.05:802:415,22:293,14:486,277,27,12
chr7 55233089 . C T . PASS AS_SB_TABLE=654,773|61,67;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=1657;AS_FilterStatus=SITE;MBQ=38,38;MFRL=175,190;MMQ=60,60;MPOS=19;POPAF=1.25;TLOD=315.93 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:1427,128:0.083:1555:742,67:513,45:654,773,61,67
chr7 55233185 . C T . PASS AS_SB_TABLE=281,468|16,57;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=846;AS_FilterStatus=SITE;MBQ=38,38;MFRL=194,213;MMQ=60,60;MPOS=17;POPAF=1.25;TLOD=197.7 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:749,73:0.092:822:425,45:280,25:281,468,16,57
chr7 55238087 . C T . PASS AS_SB_TABLE=820,970|69,71;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=2048;AS_FilterStatus=SITE;MBQ=38,38;MFRL=170,194;MMQ=60,60;MPOS=16;POPAF=0.983;TLOD=349.28 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:1790,140:0.074:1930:915,78:747,55:820,970,69,71
chr7 55238253 . G T . PASS AS_SB_TABLE=277,808|12,46;ECNT=2;GERMQ=93;SOURCES=mutect2;DP=1199;AS_FilterStatus=SITE;MBQ=38,38;MFRL=167,164;MMQ=60,60;MPOS=13;POPAF=1.92;TLOD=133.22 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:1085,58:0.053:1143:559,30:372,21:277,808,12,46
chr7 55238268 . G A . PASS AS_SB_TABLE=184,721|7,35;ECNT=2;GERMQ=93;SOURCES=mutect2;DP=997;AS_FilterStatus=SITE;MBQ=38,38;MFRL=170,174;MMQ=60,60;MPOS=19;POPAF=0.493;TLOD=94.89 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:905,42:0.048:947:430,22:285,12:184,721,7,35
chr7 55238874 . T A . PASS AS_SB_TABLE=763,465|31,18;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=1348;AS_FilterStatus=SITE;MBQ=38,38;MFRL=177,176;MMQ=60,60;MPOS=18;POPAF=0.475;TLOD=105.89 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:1228,49:0.039:1277:651,19:470,26:763,465,31,18
chr7 55240600 . C T . PASS AS_SB_TABLE=985,750|99,58;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=1960;AS_FilterStatus=SITE;MBQ=38,38;MFRL=169,155;MMQ=60,60;MPOS=21;POPAF=7.3;TLOD=397.63 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:1735,157:0.082:1892:869,73:699,65:985,750,99,58
chr7 55241707 . G A . PASS AS_SB_TABLE=310,584|62,166;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=1194;AS_FilterStatus=SITE;MBQ=38,38;MFRL=167,177;MMQ=60,60;MPOS=19;POPAF=7.3;TLOD=671.09 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:894,228:0.209:1122:429,107:346,95:310,584,62,166
chr7 55242464 MantaDEL:284:0:0:0:0:0 AGGAATTAAGAGAAGC A 0.135117 LowFisherScore;LowVafTumor SOMATIC;FETS=0.135117;TYPE=del;LEN=15;KMERSIZE=13;SB=7.65861;SOURCES=lancet;END=55242479;SVTYPE=DEL;SVLEN=-15;UPSTREAM_PAIR_COUNT=0;DOWNSTREAM_PAIR_COUNT=0;PAIR_COUNT=0;CIGAR=1M15D GT:AD:SR:SA:DP 0/1:1338,21:724,614:11,10:1359
chr7 55242609 . A G 0.277686 LowFisherScore;LowVafTumor;StrandBias SOMATIC;FETS=0.277686;TYPE=snv;LEN=1;KMERSIZE=13;SB=10.9925;SOURCES=mutect2,lancet GT:AD:SR:SA:DP 0/1:880,19:111,769:0,19:899
chr7 55242656 . T A 0 LowFisherScore;LowVafTumor;StrandBias SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=15;SB=0.145847;SOURCES=lancet GT:AD:SR:SA:DP 0/1:537,3:6,531:0,3:540
chr7 55242782 . T C 0 LowFisherScore;StrandBias SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=13;SB=0;SOURCES=lancet GT:AD:SR:SA:DP 0/1:4,25:0,4:0,25:29
chr7 55249063 . G A . PASS AS_SB_TABLE=995,648|182,115;ECNT=2;GERMQ=93;SOURCES=mutect2;DP=1992;AS_FilterStatus=SITE;MBQ=38,38;MFRL=166,161;MMQ=60,60;MPOS=17;POPAF=0.289;TLOD=825.15 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:1643,297:0.151:1940:800,150:669,111:0|1:55249063_G_A:55249063:995,648,182,115
chr7 55249071 . C T . PASS AS_SB_TABLE=1132,772|12,7;ECNT=2;GERMQ=93;SOURCES=mutect2;DP=2053;AS_FilterStatus=SITE;MBQ=38,38;MFRL=165,149;MMQ=60,60;MPOS=21;POPAF=4.13;TLOD=30.96 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 1|0:1904,19:0.011:1923:885,11:755,6:1|0:55249063_G_A:55249063:1132,772,12,7
chr7 55253305 . C A . clustered_events;haplotype AS_SB_TABLE=460,111|59,7;ECNT=5;GERMQ=93;SOURCES=mutect2;DP=650;AS_FilterStatus=SITE;MBQ=38,38;MFRL=181,193;MMQ=60,60;MPOS=19;POPAF=0.283;TLOD=252.17 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:571,66:0.112:637:259,38:248,24:0|1:55253305_C_A:55253305:460,111,59,7
chr7 55253325 . A G . clustered_events;haplotype AS_SB_TABLE=425,182|62,14;ECNT=5;GERMQ=93;SOURCES=mutect2;DP=683;AS_FilterStatus=SITE;MBQ=38,38;MFRL=170,175;MMQ=60,60;MPOS=13;POPAF=0.248;TLOD=301.06 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:607,76:0.115:683:247,39:225,28:0|1:55253305_C_A:55253305:425,182,62,14
chr7 55253338 . A T . clustered_events;haplotype AS_SB_TABLE=411,219|62,19;ECNT=5;GERMQ=93;SOURCES=mutect2;DP=711;AS_FilterStatus=SITE;MBQ=38,38;MFRL=165,164;MMQ=60,60;MPOS=20;POPAF=0.248;TLOD=339.61 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:630,81:0.118:711:259,39:231,24:0|1:55253305_C_A:55253305:411,219,62,19
chr7 55253349 . A T . clustered_events;haplotype AS_SB_TABLE=353,252|57,21;ECNT=5;GERMQ=93;SOURCES=mutect2;DP=705;AS_FilterStatus=SITE;MBQ=38,38;MFRL=164,158;MMQ=60,60;MPOS=21;POPAF=0.248;TLOD=326.23 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:605,78:0.114:683:241,37:201,23:0|1:55253305_C_A:55253305:353,252,57,21
chr7 55253425 . C T . clustered_events AS_SB_TABLE=209,548|42,87;ECNT=5;GERMQ=93;SOURCES=mutect2;DP=910;AS_FilterStatus=SITE;MBQ=38,38;MFRL=171,164;MMQ=60,60;MPOS=18;POPAF=0.257;TLOD=346.7 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:757,129:0.144:886:190,35:117,16:209,548,42,87
chr7 55259515 . T G . PASS AS_SB_TABLE=900,759|21,19;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=1847;AS_FilterStatus=SITE;MBQ=38,38;MFRL=182,169;MMQ=60,60;MPOS=17;POPAF=7.3;TLOD=71.11 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:1659,40:0.022:1699:849,21:696,12:900,759,21,19
chr7 55259763 . A G . PASS AS_SB_TABLE=282,517|74,115;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=1057;AS_FilterStatus=SITE;MBQ=38,38;MFRL=186,170;MMQ=60,60;MPOS=17;POPAF=0.181;TLOD=535.57 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:799,189:0.188:988:404,98:315,71:282,517,74,115
chr7 55260358 . G C . PASS AS_SB_TABLE=921,45|42,0;ECNT=2;GERMQ=93;SOURCES=mutect2;DP=1074;AS_FilterStatus=SITE;MBQ=38,38;MFRL=210,217;MMQ=60,60;MPOS=19;POPAF=1.59;TLOD=96.14 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:966,42:0.043:1008:491,13:445,29:921,45,42,0
chr7 55260437 MantaBND:275:0:1:0:1:0:0 C C[chr17:62792956[ . . SVTYPE=BND;MATEID=MantaBND:275:0:1:0:1:0:1;CIPOS=0,6;HOMLEN=6;HOMSEQ=CTCATC;BND_PAIR_COUNT=1;PAIR_COUNT=1 . .
chr7 55260440 . C T . PASS AS_SB_TABLE=1017,637|57,28;ECNT=2;GERMQ=93;SOURCES=mutect2;DP=1793;AS_FilterStatus=SITE;MBQ=38,38;MFRL=170,168;MMQ=60,60;MPOS=16;POPAF=1.59;TLOD=193.64 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:1654,85:0.05:1739:678,37:494,26:1017,637,57,28
chr7 55266417 . T C . PASS AS_SB_TABLE=857,587|338,213;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=2065;AS_FilterStatus=SITE;MBQ=38,38;MFRL=165,171;MMQ=60,60;MPOS=18;POPAF=0.05;TLOD=1691.35 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:1444,551:0.277:1995:694,275:591,222:857,587,338,213
chr7 55266757 . C T . PASS AS_SB_TABLE=128,296|14,48;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=499;AS_FilterStatus=SITE;MBQ=38,38;MFRL=225,241;MMQ=60,60;MPOS=20;POPAF=0.593;TLOD=177.34 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:424,62:0.131:486:234,32:174,29:128,296,14,48
chr7 55268980 . T C 1.08651 LowFisherScore SOMATIC;FETS=1.08651;TYPE=snv;LEN=1;KMERSIZE=21;SB=14.3798;SOURCES=mutect2,lancet GT:AD:SR:SA:DP 0/1:1955,556:891,1064:249,307:2511
chr7 55269675 . C CAG 12.1662 LowCovNormal;HighVafNormal;HighAltCntNormal SHARED;FETS=12.1662;TYPE=ins;LEN=2;KMERSIZE=15;SB=14.1665;SOURCES=lancet GT:AD:SR:SA:DP 0/1:1662,542:844,818:272,270:2204
chr7 55273345 . C T . PASS AS_SB_TABLE=127,972|6,68;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=1227;AS_FilterStatus=SITE;MBQ=38,38;MFRL=208,206;MMQ=60,60;MPOS=20;POPAF=2.2;TLOD=183.38 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:1099,74:0.064:1173:538,39:478,30:127,972,6,68
chr7 55276280 . G A . PASS AS_SB_TABLE=470,524|22,25;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=1098;AS_FilterStatus=SITE;MBQ=38,38;MFRL=164,172;MMQ=60,60;MPOS=13;POPAF=0.939;TLOD=110.13 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:994,47:0.047:1041:516,21:362,22:470,524,22,25
chr7 55282677 . A G . PASS AS_SB_TABLE=386,557|48,68;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=1137;AS_FilterStatus=SITE;MBQ=38,38;MFRL=167,158;MMQ=60,60;MPOS=18;POPAF=0.322;TLOD=303.07 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:943,116:0.11:1059:461,52:357,47:386,557,48,68
chr7 55292883 . T C . PASS AS_SB_TABLE=60,288|7,39;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=405;AS_FilterStatus=SITE;MBQ=38,38;MFRL=179,171;MMQ=60,60;MPOS=20;POPAF=0.485;TLOD=127.3 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:348,46:0.121:394:181,27:142,16:60,288,7,39
chr7 55324319 . T C . PASS AS_SB_TABLE=107,75|11,17;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=222;AS_FilterStatus=SITE;MBQ=38,38;MFRL=177,195;MMQ=60,60;MPOS=19;POPAF=0.562;TLOD=79 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:182,28:0.142:210:102,13:67,15:107,75,11,17
chr7 55334727 . A C . PASS AS_SB_TABLE=225,370|59,65;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=731;AS_FilterStatus=SITE;MBQ=38,38;MFRL=173,184;MMQ=60,60;MPOS=21;POPAF=0.336;TLOD=364.48 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:595,124:0.174:719:297,71:258,45:225,370,59,65
chr7 55347400 . C G . PASS AS_SB_TABLE=267,62|65,9;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=432;AS_FilterStatus=SITE;MBQ=38,38;MFRL=199,171;MMQ=60,60;MPOS=20;POPAF=0.042;TLOD=206.61 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:329,74:0.18:403:169,34:133,33:267,62,65,9
chr7 55347512 . T C . PASS AS_SB_TABLE=321,256|70,67;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=751;AS_FilterStatus=SITE;MBQ=38,38;MFRL=165,164;MMQ=60,60;MPOS=19;POPAF=0.394;TLOD=394.14 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:577,137:0.193:714:297,72:218,53:321,256,70,67
chr7 55371250 . A G . germline AS_SB_TABLE=0,0|40,417;ECNT=1;GERMQ=1;SOURCES=mutect2;DP=475;AS_FilterStatus=SITE;MBQ=0,38;MFRL=0,214;MMQ=60,60;MPOS=22;POPAF=0.267;TLOD=1825.07 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:0,457:0.998:457:0,279:0,140:0,0,40,417
chr7 55378747 . G C . germline AS_SB_TABLE=20,19|295,319;ECNT=1;GERMQ=1;SOURCES=mutect2;DP=680;AS_FilterStatus=SITE;MBQ=38,38;MFRL=156,169;MMQ=60,60;MPOS=18;POPAF=0.469;TLOD=2339.38 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:39,614:0.945:653:24,404:7,134:20,19,295,319
chr7 55378897 MantaINS:266:0:0:1:0:0 A ACCTCTCCCTCTC . . END=55378897;SVTYPE=INS;SVLEN=12;CIPOS=0,20;HOMLEN=20;HOMSEQ=CCTCTCCCTCTCCCTCTCCC;UPSTREAM_PAIR_COUNT=0;DOWNSTREAM_PAIR_COUNT=0;PAIR_COUNT=0;CIGAR=1M12I . .
chr7 55393605 . A G . germline AS_SB_TABLE=15,21|140,276;ECNT=1;GERMQ=1;SOURCES=mutect2;DP=482;AS_FilterStatus=SITE;MBQ=38,38;MFRL=182,171;MMQ=60,60;MPOS=21;POPAF=0.467;TLOD=1611 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:36,416:0.919:452:18,188:16,195:15,21,140,276
chr7 55400320 . T C . clustered_events;germline AS_SB_TABLE=0,0|175,54;ECNT=3;GERMQ=1;SOURCES=mutect2;DP=233;AS_FilterStatus=SITE;MBQ=0,38;MFRL=0,158;MMQ=60,60;MPOS=16;POPAF=0.097;TLOD=900.88 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:0,229:0.995:229:0,123:0,83:0,0,175,54
chr7 55400334 . C T . clustered_events;germline AS_SB_TABLE=14,11|168,70;ECNT=3;GERMQ=1;SOURCES=mutect2;DP=278;AS_FilterStatus=SITE;MBQ=38,38;MFRL=145,152;MMQ=60,60;MPOS=15;POPAF=0.478;TLOD=884.85 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:25,238:0.908:263:12,120:6,81:14,11,168,70
chr7 55400359 . G A . clustered_events;germline AS_SB_TABLE=0,0|144,127;ECNT=3;GERMQ=1;SOURCES=mutect2;DP=273;AS_FilterStatus=SITE;MBQ=0,38;MFRL=0,147;MMQ=60,60;MPOS=22;POPAF=0.095;TLOD=1053.41 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:0,271:0.996:271:0,118:0,80:0,0,144,127
chr7 55416964 . C T . PASS AS_SB_TABLE=332,261|75,43;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=728;AS_FilterStatus=SITE;MBQ=38,38;MFRL=163,171;MMQ=60,60;MPOS=18;POPAF=0.733;TLOD=335.59 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:593,118:0.17:711:289,65:229,41:332,261,75,43
chr7 55423050 . C T . PASS AS_SB_TABLE=238,328|50,56;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=736;AS_FilterStatus=SITE;MBQ=38,38;MFRL=172,164;MMQ=60,60;MPOS=20;POPAF=0.327;TLOD=305.76 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:566,106:0.159:672:300,56:215,42:238,328,50,56
chr7 55442202 . A G . PASS AS_SB_TABLE=300,193|49,24;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=646;AS_FilterStatus=SITE;MBQ=38,38;MFRL=175,181;MMQ=60,60;MPOS=18;POPAF=0.455;TLOD=198.14 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:493,73:0.129:566:272,39:175,28:300,193,49,24
chr7 55447747 . TCG TTA 0 LowFisherScore;StrandBias SOMATIC;FETS=0;TYPE=complex;LEN=2;KMERSIZE=17;SB=0;SOURCES=lancet GT:AD:SR:SA:DP 0/1:13,22:13,0:22,0:35
chr7 55447946 . G T 0 LowFisherScore SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=17;SB=7.05118;SOURCES=mutect2,lancet GT:AD:SR:SA:DP 0/1:28,150:22,6:118,32:178
chr7 55447988 . G T 0 LowFisherScore SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=17;SB=9.32181;SOURCES=mutect2,lancet GT:AD:SR:SA:DP 0/1:67,147:35,32:76,71:214
chr7 55448065 . T A 0 LowFisherScore;LowVafTumor;LowAltCntTumor;StrandBias SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=17;SB=2.33014;SOURCES=lancet GT:AD:SR:SA:DP 0/1:160,2:38,122:0,2:162
chr7 55448081 . A C 0 LowFisherScore SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=17;SB=9.33031;SOURCES=mutect2,lancet GT:AD:SR:SA:DP 0/1:38,92:2,36:12,80:130
chr7 55448170 . A T 0 LowFisherScore;StrandBias SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=17;SB=0;SOURCES=lancet GT:AD:SR:SA:DP 0/1:22,29:0,22:0,29:51
chr7 55457698 . C T 0 LowFisherScore;StrandBias SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=15;SB=0;SOURCES=lancet GT:AD:SR:SA:DP 0/1:31,6:31,0:6,0:37
chr7 55457756 . A C 0 LowFisherScore SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=15;SB=2.16208;SOURCES=mutect2,lancet GT:AD:SR:SA:DP 0/1:40,62:40,0:61,1:102
chr7 55457812 . T C 0 LowFisherScore;StrandBias SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=15;SB=10.2087;SOURCES=mutect2,lancet GT:AD:SR:SA:DP 0/1:109,5:67,42:5,0:114
chr7 55457861 . G A 0 LowFisherScore SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=15;SB=8.26504;SOURCES=mutect2,lancet GT:AD:SR:SA:DP 0/1:41,51:10,31:9,42:92
chr7 55457902 . C A 0 LowFisherScore;StrandBias SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=15;SB=3.71961;SOURCES=mutect2,lancet GT:AD:SR:SA:DP 0/1:31,42:1,30:0,42:73
chr7 55464067 . C T . PASS AS_SB_TABLE=67,82|181,208;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=554;AS_FilterStatus=SITE;MBQ=38,38;MFRL=164,163;MMQ=60,60;MPOS=18;POPAF=0.445;TLOD=1399.59 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:149,389:0.722:538:73,194:65,152:67,82,181,208
chr7 55471642 . A C . PASS AS_SB_TABLE=194,78|414,184;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=914;AS_FilterStatus=SITE;MBQ=38,38;MFRL=166,172;MMQ=60,60;MPOS=21;POPAF=0.449;TLOD=2117.28 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:272,598:0.691:870:126,310:118,230:194,78,414,184
chr7 55471778 . G T . PASS AS_SB_TABLE=65,191|98,359;ECNT=2;GERMQ=73;SOURCES=mutect2;DP=770;AS_FilterStatus=SITE;MBQ=38,38;MFRL=181,188;MMQ=60,60;MPOS=19;POPAF=0.447;TLOD=1654.28 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:256,457:0.648:713:132,248:106,185:65,191,98,359
chr7 55471819 . T C . PASS AS_SB_TABLE=35,142|64,266;ECNT=2;GERMQ=51;SOURCES=mutect2;DP=513;AS_FilterStatus=SITE;MBQ=38,38;MFRL=189,198;MMQ=60,60;MPOS=19;POPAF=0.447;TLOD=1183.28 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:177,330:0.659:507:73,161:63,111:35,142,64,266
chr7 116151784 . G C . PASS AS_SB_TABLE=129,266|24,46;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=483;AS_FilterStatus=SITE;MBQ=38,38;MFRL=204,207;MMQ=60,60;MPOS=11;POPAF=0.296;TLOD=198.46 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:395,70:0.152:465:222,38:139,27:129,266,24,46
chr7 116160259 . A T . PASS AS_SB_TABLE=91,173|243,343;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=894;AS_FilterStatus=SITE;MBQ=38,38;MFRL=175,172;MMQ=60,60;MPOS=19;POPAF=0.595;TLOD=2122.26 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:264,586:0.688:850:145,299:99,231:91,173,243,343
chr7 116181807 MantaDEL:297:0:0:0:5:0 CAAAAAAAA C . . END=116181815;SVTYPE=DEL;SVLEN=-8;CIPOS=0,11;HOMLEN=11;HOMSEQ=AAAAAAAAAAA;UPSTREAM_PAIR_COUNT=0;DOWNSTREAM_PAIR_COUNT=0;PAIR_COUNT=0;CIGAR=1M8D . .
chr7 116182054 . C T . PASS AS_SB_TABLE=31,38|198,207;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=536;AS_FilterStatus=SITE;MBQ=38,38;MFRL=159,169;MMQ=60,60;MPOS=17;POPAF=0.099;TLOD=1560.1 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:69,405:0.863:474:30,235:24,136:31,38,198,207
chr7 116194228 . T A 0 LowFisherScore SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=15;SB=10.4558;SOURCES=mutect2,lancet GT:AD:SR:SA:DP 0/1:127,202:65,62:104,98:329
chr7 116194284 . A G 0 LowFisherScore SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=15;SB=14.7118;SOURCES=mutect2,lancet GT:AD:SR:SA:DP 0/1:242,23:64,178:2,21:265
chr7 116194298 . A G 0 LowFisherScore;LowVafTumor;LowAltCntTumor;StrandBias SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=13;SB=1.49953;SOURCES=lancet GT:AD:SR:SA:DP 0/1:276,2:44,232:0,2:278
chr7 116194384 . C T 0 LowFisherScore;StrandBias SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=13;SB=0;SOURCES=lancet GT:AD:SR:SA:DP 0/1:39,83:0,39:0,83:122
chr7 116204058 . T C . PASS AS_SB_TABLE=163,41|411,147;ECNT=2;GERMQ=93;SOURCES=mutect2;DP=811;AS_FilterStatus=SITE;MBQ=38,38;MFRL=190,183;MMQ=60,60;MPOS=13;POPAF=0.733;TLOD=2022.79 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:204,558:0.728:762:92,281:98,231:163,41,411,147
chr7 116204090 . G A . PASS AS_SB_TABLE=510,313|85,36;ECNT=2;GERMQ=93;SOURCES=mutect2;DP=975;AS_FilterStatus=SITE;MBQ=38,38;MFRL=170,175;MMQ=60,60;MPOS=22;POPAF=0.217;TLOD=342.31 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:823,121:0.133:944:374,54:318,51:510,313,85,36
chr7 116217657 . G A . PASS AS_SB_TABLE=317,259|78,51;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=733;AS_FilterStatus=SITE;MBQ=38,38;MFRL=167,172;MMQ=60,60;MPOS=21;POPAF=0.237;TLOD=373.95 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:576,129:0.182:705:333,71:181,46:317,259,78,51
chr7 116226375 . C T . PASS AS_SB_TABLE=237,209|17,15;ECNT=2;GERMQ=93;SOURCES=mutect2;DP=488;AS_FilterStatus=SITE;MBQ=38,38;MFRL=171,175;MMQ=60,60;MPOS=19;POPAF=7.3;TLOD=80.27 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:446,32:0.072:478:224,18:179,13:237,209,17,15
chr7 116226422 . G A . PASS AS_SB_TABLE=26,32|107,277;ECNT=2;GERMQ=93;SOURCES=mutect2;DP=452;AS_FilterStatus=SITE;MBQ=38,38;MFRL=170,181;MMQ=60,60;MPOS=14;POPAF=0.217;TLOD=1454.55 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:58,384:0.873:442:29,146:13,130:26,32,107,277
chr7 116246824 . A G 0 LowFisherScore SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=15;SB=11.0663;SOURCES=mutect2,lancet GT:AD:SR:SA:DP 0/1:26,216:12,14:73,143:242
chr7 116256816 . T C . PASS AS_SB_TABLE=246,257|24,34;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=577;AS_FilterStatus=SITE;MBQ=38,38;MFRL=185,188;MMQ=60,60;MPOS=16;POPAF=0.622;TLOD=157.6 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:503,58:0.104:561:296,28:186,27:246,257,24,34
chr7 116266607 . G C . PASS AS_SB_TABLE=334,77|27,6;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=448;AS_FilterStatus=SITE;MBQ=38,38;MFRL=210,197;MMQ=60,60;MPOS=18;POPAF=0.614;TLOD=82.4 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:411,33:0.077:444:234,17:159,15:334,77,27,6
chr7 116266694 . C T . PASS AS_SB_TABLE=332,260|37,26;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=669;AS_FilterStatus=SITE;MBQ=38,38;MFRL=182,178;MMQ=60,60;MPOS=18;POPAF=0.614;TLOD=153.58 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:592,63:0.094:655:340,39:204,18:332,260,37,26
chr7 116266792 . A G . PASS AS_SB_TABLE=26,476|3,45;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=573;AS_FilterStatus=SITE;MBQ=38,38;MFRL=210,212;MMQ=60,60;MPOS=25;POPAF=0.614;TLOD=124.76 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:502,48:0.087:550:288,25:198,21:26,476,3,45
chr7 116293225 . C T . PASS AS_SB_TABLE=210,431|20,41;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=717;AS_FilterStatus=SITE;MBQ=38,38;MFRL=179,187;MMQ=60,60;MPOS=15;POPAF=0.607;TLOD=167.29 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:641,61:0.092:702:360,33:236,26:210,431,20,41
chr7 116309236 . C T . PASS AS_SB_TABLE=44,378|4,37;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=476;AS_FilterStatus=SITE;MBQ=38,38;MFRL=216,220;MMQ=60,60;MPOS=14;POPAF=1.89;TLOD=108.54 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:422,41:0.093:463:233,30:165,11:44,378,4,37
chr7 116315205 . T C . PASS AS_SB_TABLE=210,165|25,18;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=473;AS_FilterStatus=SITE;MBQ=38,38;MFRL=172,182;MMQ=60,60;MPOS=19;POPAF=0.684;TLOD=114.97 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:375,43:0.109:418:212,25:128,16:210,165,25,18
chr7 116319211 . C T . PASS AS_SB_TABLE=94,69|11,4;ECNT=2;GERMQ=93;SOURCES=mutect2;DP=183;AS_FilterStatus=SITE;MBQ=38,38;MFRL=171,191;MMQ=60,60;MPOS=15;POPAF=0.223;TLOD=43.91 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:163,15:0.089:178:86,10:63,5:0|1:116319211_C_T:116319211:94,69,11,4
chr7 116319214 . C T . PASS AS_SB_TABLE=93,69|11,4;ECNT=2;GERMQ=93;SOURCES=mutect2;DP=183;AS_FilterStatus=SITE;MBQ=38,38;MFRL=171,191;MMQ=60,60;MPOS=18;POPAF=0.23;TLOD=43.86 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:162,15:0.089:177:88,10:61,5:0|1:116319211_C_T:116319211:93,69,11,4
chr7 116327264 . T C . PASS AS_SB_TABLE=228,415|10,21;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=714;AS_FilterStatus=SITE;MBQ=38,38;MFRL=181,163;MMQ=60,60;MPOS=21;POPAF=7.3;TLOD=66.26 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:643,31:0.044:674:337,12:242,13:228,415,10,21
chr7 116335854 . G A . PASS AS_SB_TABLE=219,237|208,196;ECNT=1;GERMQ=21;SOURCES=mutect2;DP=946;AS_FilterStatus=SITE;MBQ=38,38;MFRL=211,202;MMQ=60,60;MPOS=16;POPAF=7.3;TLOD=1386.38 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:456,404:0.469:860:236,213:204,176:219,237,208,196
chr7 116336880 . T C 0 LowFisherScore;StrandBias SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=15;SB=0;SOURCES=lancet GT:AD:SR:SA:DP 0/1:3,19:3,0:19,0:22
chr7 116336947 . C T 0 LowFisherScore;StrandBias SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=15;SB=0.636691;SOURCES=lancet GT:AD:SR:SA:DP 0/1:95,15:94,1:15,0:110
chr7 116336948 . G A 0 LowFisherScore SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=15;SB=5.05667;SOURCES=lancet GT:AD:SR:SA:DP 0/1:22,93:21,1:92,1:115
chr7 116337144 . G A 6.21923 LowCovNormal SOMATIC;FETS=6.21923;TYPE=snv;LEN=1;KMERSIZE=15;SB=11.9423;SOURCES=mutect2,lancet GT:AD:SR:SA:DP 0/1:202,647:110,92:349,298:849
chr7 116337192 . G A 0.0121822 LowFisherScore;LowVafTumor;LowAltCntTumor SOMATIC;FETS=0.0121822;TYPE=snv;LEN=1;KMERSIZE=13;SB=3.07553;SOURCES=lancet GT:AD:SR:SA:DP 0/1:711,2:310,401:1,1:713
chr7 116337223 . T A 0 LowFisherScore;LowVafTumor;LowAltCntTumor;StrandBias SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=13;SB=3.08428;SOURCES=lancet GT:AD:SR:SA:DP 0/1:584,2:175,409:0,2:586
chr7 116337243 . T A 0 LowFisherScore;LowVafTumor;LowAltCntTumor;StrandBias SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=13;SB=1.36128;SOURCES=lancet GT:AD:SR:SA:DP 0/1:550,2:80,470:0,2:552
chr7 116337258 . G A 0.0175119 LowFisherScore;LowVafTumor;LowAltCntTumor;StrandBias SOMATIC;FETS=0.0175119;TYPE=snv;LEN=1;KMERSIZE=13;SB=0.194998;SOURCES=lancet GT:AD:SR:SA:DP 0/1:494,2:11,483:0,2:496
chr7 116337269 . CT C 0.0180956 LowFisherScore;LowVafTumor;LowAltCntTumor;StrandBias SOMATIC;FETS=0.0180956;TYPE=del;LEN=1;KMERSIZE=13;SB=0;SOURCES=lancet GT:AD:SR:SA:DP 0/1:478,2:0,478:0,2:480
chr7 116337287 . G A 0.030335 LowFisherScore;LowVafTumor;StrandBias SOMATIC;FETS=0.030335;TYPE=snv;LEN=1;KMERSIZE=13;SB=0;SOURCES=lancet GT:AD:SR:SA:DP 0/1:427,3:0,427:0,3:430
chr7 116337352 . T G 5.94235 LowCovNormal;StrandBias SOMATIC;FETS=5.94235;TYPE=snv;LEN=1;KMERSIZE=15;SB=0;SOURCES=lancet GT:AD:SR:SA:DP 0/1:27,82:0,27:0,82:109
chr7 116339847 . GT G 0.775604 LowFisherScore SOMATIC;FETS=0.775604;TYPE=del;LEN=1;KMERSIZE=15;SB=11.6187;SOURCES=lancet GT:AD:SR:SA:DP 0/1:1987,122:997,990:59,63:2109
chr7 116341383 . A G . PASS AS_SB_TABLE=47,1|149,0;ECNT=1;GERMQ=73;SOURCES=mutect2;DP=217;AS_FilterStatus=SITE;MBQ=38,38;MFRL=215,223;MMQ=60,60;MPOS=22;POPAF=0.614;TLOD=579.54 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:48,149:0.755:197:30,86:16,63:47,1,149,0
chr7 116341488 . G A . PASS AS_SB_TABLE=46,56|140,144;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=415;AS_FilterStatus=SITE;MBQ=38,38;MFRL=185,190;MMQ=60,60;MPOS=21;POPAF=0.614;TLOD=1051.87 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:102,284:0.742:386:47,161:42,99:46,56,140,144
chr7 116342627 . G T . PASS AS_SB_TABLE=33,17|116,46;ECNT=1;GERMQ=91;SOURCES=mutect2;DP=222;AS_FilterStatus=SITE;MBQ=38,38;MFRL=171,174;MMQ=60,60;MPOS=21;POPAF=0.614;TLOD=626.46 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:50,162:0.765:212:29,100:17,55:33,17,116,46
chr7 116344098 . T C . PASS AS_SB_TABLE=137,61|402,180;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=791;AS_FilterStatus=SITE;MBQ=38,38;MFRL=156,163;MMQ=60,60;MPOS=19;POPAF=0.616;TLOD=2101.78 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:198,582:0.752:780:108,295:57,217:137,61,402,180
chr7 116351073 . G A . PASS AS_SB_TABLE=539,173|32,12;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=799;AS_FilterStatus=SITE;MBQ=38,38;MFRL=220,247;MMQ=60,60;MPOS=19;POPAF=7.3;TLOD=107.14 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:712,44:0.06:756:376,24:319,20:539,173,32,12
chr7 116351272 . C T . PASS AS_SB_TABLE=374,550|19,15;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=1026;AS_FilterStatus=SITE;MBQ=38,38;MFRL=197,200;MMQ=60,60;MPOS=22;POPAF=7.3;TLOD=77.87 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:924,34:0.037:958:511,24:349,9:374,550,19,15
chr7 116354525 . T A . PASS AS_SB_TABLE=309,305|20,17;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=681;AS_FilterStatus=SITE;MBQ=38,38;MFRL=151,141;MMQ=60,60;MPOS=19;POPAF=0.385;TLOD=73.33 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:614,37:0.053:651:297,16:212,12:309,305,20,17
chr7 116357211 . C T 0 LowFisherScore;StrandBias SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=13;SB=0;SOURCES=lancet GT:AD:SR:SA:DP 0/1:24,7:24,0:7,0:31
chr7 116357368 . A G 0 LowFisherScore SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=15;SB=8.85816;SOURCES=mutect2,lancet GT:AD:SR:SA:DP 0/1:16,199:12,4:123,76:215
chr7 116374866 . T C . PASS AS_SB_TABLE=469,355|29,20;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=914;AS_FilterStatus=SITE;MBQ=38,38;MFRL=181,171;MMQ=60,60;MPOS=24;POPAF=7.3;TLOD=116.67 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:824,49:0.057:873:477,23:255,20:469,355,29,20
chr7 116375102 . C T . PASS AS_SB_TABLE=81,312|10,68;ECNT=2;GERMQ=93;SOURCES=mutect2;DP=508;AS_FilterStatus=SITE;MBQ=33,34;MFRL=197,229;MMQ=60,60;MPOS=13;POPAF=4.31;TLOD=183.51 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:393,78:0.17:471:207,44:81,14:81,312,10,68
chr7 116375106 . A G . base_qual;strand_bias AS_SB_TABLE=80,312|0,28;ECNT=2;GERMQ=93;SOURCES=mutect2;DP=488;AS_FilterStatus=base_qual;MBQ=31,10;MFRL=204,221;MMQ=60,60;MPOS=17;POPAF=7.3;TLOD=6.24 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:392,28:0.031:420:201,0:80,6:80,312,0,28
chr7 116397572 . A G . PASS AS_SB_TABLE=76,82|473,457;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=1151;AS_FilterStatus=SITE;MBQ=38,38;MFRL=186,189;MMQ=60,60;MPOS=18;POPAF=0.759;TLOD=3473.72 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:158,930:0.853:1088:87,494:59,348:76,82,473,457
chr7 116399131 . G A . PASS AS_SB_TABLE=237,399|10,23;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=694;AS_FilterStatus=SITE;MBQ=38,38;MFRL=205,216;MMQ=60,60;MPOS=17;POPAF=0.5;TLOD=81.52 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:636,33:0.052:669:354,18:249,15:237,399,10,23
chr7 116409653 . A T 0 LowFisherScore;LowVafTumor;LowAltCntTumor;StrandBias SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=19;SB=0;SOURCES=lancet GT:AD:SR:SA:DP 0/1:265,2:265,0:2,0:267
chr7 116414149 . A G 0 LowFisherScore;LowVafTumor;LowAltCntTumor;StrandBias SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=17;SB=2.97707;SOURCES=lancet GT:AD:SR:SA:DP 0/1:574,2:167,407:0,2:576
chr7 116421967 . T C . germline AS_SB_TABLE=6,0|219,0;ECNT=1;GERMQ=1;SOURCES=mutect2;DP=241;AS_FilterStatus=SITE;MBQ=38,38;MFRL=328,274;MMQ=60,60;MPOS=22;POPAF=0.19;TLOD=902.59 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:6,219:0.969:225:3,129:3,88:6,0,219,0
chr7 116422214 . C T . PASS AS_SB_TABLE=150,526|20,64;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=811;AS_FilterStatus=SITE;MBQ=38,38;MFRL=187,206;MMQ=60,60;MPOS=16;POPAF=1.8;TLOD=223.04 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:676,84:0.111:760:341,42:281,36:150,526,20,64
chr7 116423161 . G A . PASS AS_SB_TABLE=38,62|105,228;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=478;AS_FilterStatus=SITE;MBQ=38,38;MFRL=256,247;MMQ=60,60;MPOS=13;POPAF=0.815;TLOD=1292.31 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:100,333:0.769:433:65,195:33,124:38,62,105,228
chr7 116423320 . A G . PASS AS_SB_TABLE=519,49|71,5;ECNT=2;GERMQ=93;SOURCES=mutect2;DP=674;AS_FilterStatus=SITE;MBQ=38,38;MFRL=218,208;MMQ=60,60;MPOS=21;POPAF=1.74;TLOD=216.26 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:568,76:0.119:644:316,42:237,32:519,49,71,5
chr7 116423332 . G T . PASS AS_SB_TABLE=614,105|9,0;ECNT=2;GERMQ=93;SOURCES=mutect2;DP=748;AS_FilterStatus=SITE;MBQ=38,38;MFRL=206,205;MMQ=60,60;MPOS=11;POPAF=4.61;TLOD=8.17 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:719,9:0.014:728:371,3:288,6:614,105,9,0
chr7 116431427 . C T . germline AS_SB_TABLE=6,25|233,440;ECNT=1;GERMQ=1;SOURCES=mutect2;DP=754;AS_FilterStatus=SITE;MBQ=38,38;MFRL=169,162;MMQ=60,60;MPOS=18;POPAF=0.166;TLOD=2604.33 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:31,673:0.952:704:20,353:11,245:6,25,233,440
chr7 116435691 MantaBND:304:0:1:0:1:0:1 T ]chr16:13844759]T . . SVTYPE=BND;MATEID=MantaBND:304:0:1:0:1:0:0;CIPOS=0,8;HOMLEN=8;HOMSEQ=GTTTCTTG;BND_PAIR_COUNT=1;PAIR_COUNT=1 . .
chr7 116435768 . C T . PASS AS_SB_TABLE=1150,653|64,36;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=1996;AS_FilterStatus=SITE;MBQ=38,38;MFRL=188,181;MMQ=60,60;MPOS=19;POPAF=0.45;TLOD=242.93 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:1803,100:0.054:1903:925,54:747,39:1150,653,64,36
chr7 116436022 . G A . PASS AS_SB_TABLE=1091,1090|67,86;ECNT=2;GERMQ=93;SOURCES=mutect2;DP=2436;AS_FilterStatus=SITE;MBQ=38,38;MFRL=184,176;MMQ=60,60;MPOS=20;POPAF=0.447;TLOD=372.62 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:2181,153:0.065:2334:1072,62:964,78:1091,1090,67,86
chr7 116436097 . G A . PASS AS_SB_TABLE=862,1154|58,73;ECNT=2;GERMQ=93;SOURCES=mutect2;DP=2283;AS_FilterStatus=SITE;MBQ=38,38;MFRL=184,182;MMQ=60,60;MPOS=19;POPAF=0.447;TLOD=323.16 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:2016,131:0.061:2147:815,57:751,47:862,1154,58,73
chr7 116437504 . A G . PASS AS_SB_TABLE=155,14|12,1;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=191;AS_FilterStatus=SITE;MBQ=38,38;MFRL=171,152;MMQ=60,60;MPOS=17;POPAF=0.447;TLOD=30.18 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:169,13:0.071:182:101,10:65,2:155,14,12,1
chr7 116437606 . G A . germline AS_SB_TABLE=6,19|93,337;ECNT=1;GERMQ=1;SOURCES=mutect2;DP=472;AS_FilterStatus=SITE;MBQ=34,38;MFRL=141,172;MMQ=60,60;MPOS=16;POPAF=0.195;TLOD=1567.37 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:25,430:0.947:455:12,220:5,149:6,19,93,337
chr7 116449000 . G A . germline AS_SB_TABLE=11,15|209,112;ECNT=2;GERMQ=1;SOURCES=mutect2;DP=364;AS_FilterStatus=SITE;MBQ=38,38;MFRL=183,176;MMQ=60,60;MPOS=12;POPAF=0.201;TLOD=1199.19 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:26,321:0.921:347:9,192:15,95:11,15,209,112
chr7 116449050 . T C . PASS AS_SB_TABLE=131,244|8,11;ECNT=2;GERMQ=93;SOURCES=mutect2;DP=410;AS_FilterStatus=SITE;MBQ=38,38;MFRL=178,184;MMQ=60,60;MPOS=22;POPAF=0.455;TLOD=45.83 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:375,19:0.052:394:152,9:124,7:131,244,8,11
chr7 116456018 . G A . PASS AS_SB_TABLE=90,54|7,3;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=159;AS_FilterStatus=SITE;MBQ=38,36;MFRL=212,149;MMQ=60,60;MPOS=21;POPAF=0.452;TLOD=20.41 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:144,10:0.062:154:74,4:62,4:90,54,7,3
chr7 116456123 . A G . PASS AS_SB_TABLE=9,97|0,6;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=113;AS_FilterStatus=SITE;MBQ=38,38;MFRL=234,255;MMQ=60,60;MPOS=16;POPAF=0.452;TLOD=14.13 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:106,6:0.061:112:60,2:44,4:9,97,0,6
chr7 116468914 . G A . germline AS_SB_TABLE=6,11|120,219;ECNT=1;GERMQ=1;SOURCES=mutect2;DP=378;AS_FilterStatus=SITE;MBQ=38,38;MFRL=197,191;MMQ=60,60;MPOS=17;POPAF=0.257;TLOD=1366.76 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:17,339:0.949:356:12,207:4,120:6,11,120,219
chr7 116481034 . G A . germline AS_SB_TABLE=16,18|107,178;ECNT=1;GERMQ=1;SOURCES=mutect2;DP=324;AS_FilterStatus=SITE;MBQ=38,38;MFRL=169,198;MMQ=60,60;MPOS=13;POPAF=0.195;TLOD=1108.89 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:34,285:0.902:319:12,165:16,96:16,18,107,178
chr7 116491991 . T C . germline AS_SB_TABLE=11,16|165,434;ECNT=1;GERMQ=1;SOURCES=mutect2;DP=641;AS_FilterStatus=SITE;MBQ=38,38;MFRL=188,181;MMQ=60,60;MPOS=17;POPAF=0.225;TLOD=2317.71 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:27,599:0.956:626:15,303:10,243:11,16,165,434
chr7 116528240 . C T . PASS AS_SB_TABLE=19,66|34,246;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=388;AS_FilterStatus=SITE;MBQ=38,38;MFRL=181,189;MMQ=60,60;MPOS=24;POPAF=0.572;TLOD=1073.67 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:85,280:0.767:365:48,166:32,97:19,66,34,246
chr7 116547015 . C T . PASS AS_SB_TABLE=20,50|52,156;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=290;AS_FilterStatus=SITE;MBQ=38,38;MFRL=190,203;MMQ=60,60;MPOS=14;POPAF=0.559;TLOD=785.29 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:70,208:0.754:278:31,123:33,76:20,50,52,156
chr7 116562288 . G C . PASS AS_SB_TABLE=110,46|290,154;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=615;AS_FilterStatus=SITE;MBQ=38,38;MFRL=186,177;MMQ=60,60;MPOS=14;POPAF=0.564;TLOD=1624.67 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:156,444:0.734:600:84,244:61,162:110,46,290,154
chr7 116589815 . C T . PASS AS_SB_TABLE=321,924|11,40;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=1327;AS_FilterStatus=SITE;MBQ=38,38;MFRL=180,187;MMQ=60,60;MPOS=15;POPAF=7.3;TLOD=112.93 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:1245,51:0.04:1296:632,31:493,13:321,924,11,40
chr7 116635705 . C T . PASS AS_SB_TABLE=466,592|65,85;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=1270;AS_FilterStatus=SITE;MBQ=38,38;MFRL=173,175;MMQ=60,60;MPOS=18;POPAF=0.293;TLOD=414.2 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:1058,150:0.126:1208:554,77:396,59:466,592,65,85
chr7 128767145 MantaBND:321:0:1:0:2:0:0 C C]chr10:50668596] . . SVTYPE=BND;MATEID=MantaBND:321:0:1:0:2:0:1;CIPOS=0,7;HOMLEN=7;HOMSEQ=GAAATGT;BND_PAIR_COUNT=1;PAIR_COUNT=1 . .
chr7 140434505 . G A 0 LowFisherScore;LowVafTumor;StrandBias SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=31;SB=1.96277;SOURCES=lancet GT:AD:SR:SA:DP 0/1:663,3:93,570:0,3:666
chr7 140439695 . G A 0.022918 LowFisherScore;LowVafTumor;LowAltCntTumor;StrandBias SOMATIC;FETS=0.022918;TYPE=snv;LEN=1;KMERSIZE=19;SB=9.72804;SOURCES=lancet GT:AD:SR:SA:DP 0/1:377,2:122,255:2,0:379
chr7 140439741 . A G 0.413927 LowFisherScore SOMATIC;FETS=0.413927;TYPE=snv;LEN=1;KMERSIZE=15;SB=8.34298;SOURCES=mutect2,lancet GT:AD:SR:SA:DP 0/1:469,47:84,385:7,40:516
chr7 140439806 . T A 0 LowFisherScore;LowVafTumor;LowAltCntTumor;StrandBias SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=19;SB=0;SOURCES=lancet GT:AD:SR:SA:DP 0/1:314,2:0,314:0,2:316
chr7 140439987 . T A 0 LowFisherScore;StrandBias SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=19;SB=0;SOURCES=lancet GT:AD:SR:SA:DP 0/1:17,6:0,17:0,6:23
chr7 140439988 . GC G 0 LowFisherScore;StrandBias SOMATIC;FETS=0;TYPE=del;LEN=1;KMERSIZE=19;SB=0;SOURCES=lancet GT:AD:SR:SA:DP 0/1:13,5:0,13:0,5:18
chr7 140449071 . C G . PASS AS_SB_TABLE=322,66|63,12;ECNT=2;GERMQ=93;SOURCES=mutect2;DP=494;AS_FilterStatus=SITE;MBQ=38,38;MFRL=188,177;MMQ=60,60;MPOS=15;POPAF=0.569;TLOD=208.98 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:388,75:0.162:463:213,39:145,29:322,66,63,12
chr7 140449150 . T C . PASS AS_SB_TABLE=198,272|51,62;ECNT=2;GERMQ=93;SOURCES=mutect2;DP=623;AS_FilterStatus=SITE;MBQ=38,38;MFRL=172,169;MMQ=60,50;MPOS=18;POPAF=0.564;TLOD=319.68 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:470,113:0.191:583:182,47:109,22:198,272,51,62
chr7 140453136 . A T . PASS AS_SB_TABLE=247,451|22,45;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=804;AS_FilterStatus=SITE;MBQ=38,38;MFRL=161,162;MMQ=60,60;MPOS=19;POPAF=7.3;TLOD=172.07 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:698,67:0.089:765:394,39:227,22:247,451,22,45
chr7 140476794 . A G . PASS AS_SB_TABLE=675,718|28,26;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=1491;AS_FilterStatus=SITE;MBQ=38,38;MFRL=174,186;MMQ=60,60;MPOS=21;POPAF=7.3;TLOD=115.91 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:1393,54:0.038:1447:684,23:534,25:675,718,28,26
chr7 140476936 . G A . PASS AS_SB_TABLE=2,254|0,31;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=297;AS_FilterStatus=SITE;MBQ=38,38;MFRL=220,220;MMQ=60,60;MPOS=21;POPAF=1.23;TLOD=85.6 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:256,31:0.111:287:142,15:113,16:2,254,0,31
chr7 140482110 . A T 0 LowFisherScore;LowVafTumor;LowAltCntTumor;StrandBias SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=21;SB=0.998158;SOURCES=lancet GT:AD:SR:SA:DP 0/1:238,2:212,26:2,0:240
chr7 140482146 . G A 0 LowFisherScore;LowVafTumor;LowAltCntTumor;StrandBias SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=21;SB=9.97427;SOURCES=lancet GT:AD:SR:SA:DP 0/1:246,2:169,77:0,2:248
chr7 140482427 . T C 0 LowFisherScore SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=13;SB=10.0717;SOURCES=mutect2,lancet GT:AD:SR:SA:DP 0/1:316,38:276,40:36,2:354
chr7 140482926 . AG A 0.872107 LowFisherScore SOMATIC;FETS=0.872107;TYPE=del;LEN=1;KMERSIZE=13;SB=16.0981;SOURCES=lancet GT:AD:SR:SA:DP 0/1:1627,172:724,903:67,105:1799
chr7 140483331 . T A 0 LowFisherScore SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=15;SB=5.23253;SOURCES=mutect2,lancet GT:AD:SR:SA:DP 0/1:94,14:2,92:1,13:108
chr7 140483400 . T C 0 LowFisherScore SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=15;SB=7.53718;SOURCES=mutect2,lancet GT:AD:SR:SA:DP 0/1:158,28:149,9:25,3:186
chr7 140483403 . C T 0 LowFisherScore;StrandBias SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=15;SB=4.1104;SOURCES=mutect2,lancet GT:AD:SR:SA:DP 0/1:172,15:161,11:15,0:187
chr7 140483605 . C T 0.465637 LowFisherScore SOMATIC;FETS=0.465637;TYPE=snv;LEN=1;KMERSIZE=15;SB=18.0134;SOURCES=mutect2,lancet GT:AD:SR:SA:DP 0/1:591,67:398,193:53,14:658
chr7 140484253 . T A 0.027989 LowFisherScore;LowVafTumor;StrandBias SOMATIC;FETS=0.027989;TYPE=snv;LEN=1;KMERSIZE=19;SB=3.2264;SOURCES=lancet GT:AD:SR:SA:DP 0/1:463,3:102,361:0,3:466
chr7 140485335 . T C . PASS AS_SB_TABLE=624,453|129,103;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=1409;AS_FilterStatus=SITE;MBQ=38,38;MFRL=214,193;MMQ=60,60;MPOS=15;POPAF=0.569;TLOD=678.53 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:1077,232:0.176:1309:637,121:380,97:624,453,129,103
chr7 140485690 . C T 0 LowFisherScore SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=15;SB=14.8175;SOURCES=mutect2,lancet GT:AD:SR:SA:DP 0/1:566,118:375,191:86,32:684
chr7 140486288 . C T 0.775584 LowFisherScore SOMATIC;FETS=0.775584;TYPE=snv;LEN=1;KMERSIZE=13;SB=11.7587;SOURCES=mutect2,lancet GT:AD:SR:SA:DP 0/1:848,166:356,492:68,98:1014
chr7 140486513 . A G . PASS AS_SB_TABLE=422,524|21,38;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=1035;AS_FilterStatus=SITE;MBQ=38,38;MFRL=227,201;MMQ=60,60;MPOS=21;POPAF=1.23;TLOD=144.97 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:946,59:0.059:1005:556,33:364,21:422,524,21,38
chr7 140486743 . T C 0 LowFisherScore SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=27;SB=9.1499;SOURCES=mutect2,lancet GT:AD:SR:SA:DP 0/1:283,18:67,216:2,16:301
chr7 140487100 MantaDEL:329:0:0:0:0:0 CAAAAAAAAAA C . . END=140487110;SVTYPE=DEL;SVLEN=-10;CIPOS=0,14;HOMLEN=14;HOMSEQ=AAAAAAAAAAAAAA;UPSTREAM_PAIR_COUNT=0;DOWNSTREAM_PAIR_COUNT=0;PAIR_COUNT=0;CIGAR=1M10D . .
chr7 140487202 . C T 0 LowFisherScore SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=27;SB=4.49763;SOURCES=mutect2,lancet GT:AD:SR:SA:DP 0/1:199,41:197,2:40,1:240
chr7 140488156 . T G 0 LowFisherScore SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=15;SB=5.04808;SOURCES=mutect2,lancet GT:AD:SR:SA:DP 0/1:112,18:2,110:1,17:130
chr7 140490207 . T C . PASS AS_SB_TABLE=88,162|204,353;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=834;AS_FilterStatus=SITE;MBQ=38,38;MFRL=243,238;MMQ=60,60;MPOS=17;POPAF=0.983;TLOD=2068.06 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:250,557:0.696:807:129,299:107,237:88,162,204,353
chr7 140490382 . C T . PASS AS_SB_TABLE=585,351|114,58;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=1126;AS_FilterStatus=SITE;MBQ=38,38;MFRL=199,242;MMQ=60,60;MPOS=18;POPAF=0.569;TLOD=508.83 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:936,172:0.163:1108:506,109:343,59:585,351,114,58
chr7 140490928 . C A 0 LowFisherScore SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=21;SB=10.0467;SOURCES=mutect2,lancet GT:AD:SR:SA:DP 0/1:414,74:412,2:72,2:488
chr7 140491258 . C T 0.323848 LowFisherScore SOMATIC;FETS=0.323848;TYPE=snv;LEN=1;KMERSIZE=35;SB=10.7344;SOURCES=mutect2,lancet GT:AD:SR:SA:DP 0/1:1239,96:579,660:45,51:1335
chr7 140491331 . T TCAATTTACATATGCTCTTTGAG 0 LowFisherScore SOMATIC;FETS=0;TYPE=ins;LEN=22;KMERSIZE=35;SB=20.8904;SOURCES=lancet GT:AD:SR:SA:DP 0/1:1111,78:469,642:23,55:1189
chr7 140491678 . G A 0 LowFisherScore SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=13;SB=12.3379;SOURCES=mutect2,lancet GT:AD:SR:SA:DP 0/1:796,187:360,436:81,106:983
chr7 140492039 . T C . PASS AS_SB_TABLE=631,679|104,89;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=1634;AS_FilterStatus=SITE;MBQ=38,38;MFRL=201,215;MMQ=60,60;MPOS=17;POPAF=0.987;TLOD=540.42 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:1310,193:0.129:1503:666,105:587,81:631,679,104,89
chr7 140492411 . T C . PASS AS_SB_TABLE=568,981|45,71;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=1693;AS_FilterStatus=SITE;MBQ=38,38;MFRL=195,207;MMQ=60,60;MPOS=22;POPAF=1.23;TLOD=292.2 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:1549,116:0.07:1665:800,58:643,51:568,981,45,71
chr7 140493029 . A G . PASS AS_SB_TABLE=482,501|37,36;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=1120;AS_FilterStatus=SITE;MBQ=38,38;MFRL=198,188;MMQ=60,60;MPOS=15;POPAF=1.23;TLOD=186.23 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:983,73:0.069:1056:538,45:399,25:482,501,37,36
chr7 140494209 . G A 0 LowFisherScore SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=15;SB=19.2357;SOURCES=mutect2,lancet GT:AD:SR:SA:DP 0/1:661,161:284,377:56,105:822
chr7 140500135 . C T . PASS AS_SB_TABLE=499,187|30,7;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=765;AS_FilterStatus=SITE;MBQ=38,38;MFRL=169,185;MMQ=60,60;MPOS=15;POPAF=1.24;TLOD=93.72 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:686,37:0.056:723:343,20:282,16:499,187,30,7
chr7 140507664 . A T 0 LowFisherScore;LowVafTumor;LowAltCntTumor;StrandBias SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=17;SB=0;SOURCES=lancet GT:AD:SR:SA:DP 0/1:129,2:129,0:2,0:131
chr7 140507800 . A T 0 LowFisherScore;LowVafTumor;LowAltCntTumor SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=17;SB=4.7762;SOURCES=lancet GT:AD:SR:SA:DP 0/1:388,2:307,81:1,1:390
chr7 140507937 . A T 0 LowFisherScore;StrandBias SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=15;SB=4.63974;SOURCES=mutect2,lancet GT:AD:SR:SA:DP 0/1:355,18:21,334:0,18:373
chr7 140507940 . A T 0 LowFisherScore;LowVafTumor;StrandBias SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=15;SB=1.13983;SOURCES=mutect2,lancet GT:AD:SR:SA:DP 0/1:349,5:18,331:0,5:354
chr7 140508151 MantaDEL:324:0:0:0:0:0 CAAAAAAAAAAAA C . . END=140508163;SVTYPE=DEL;SVLEN=-12;CIPOS=0,14;HOMLEN=14;HOMSEQ=AAAAAAAAAAAAAA;UPSTREAM_PAIR_COUNT=0;DOWNSTREAM_PAIR_COUNT=0;PAIR_COUNT=0;CIGAR=1M12D . .
chr8 38100688 . G A . PASS AS_SB_TABLE=139,290|15,38;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=517;AS_FilterStatus=SITE;MBQ=38,38;MFRL=189,199;MMQ=60,60;MPOS=14;POPAF=0.666;TLOD=144.26 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:429,53:0.115:482:217,28:185,21:139,290,15,38
chr8 38120721 . T C . PASS AS_SB_TABLE=65,7|13,1;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=97;AS_FilterStatus=SITE;MBQ=38,38;MFRL=201,204;MMQ=60,60;MPOS=24;POPAF=7.3;TLOD=42.26 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:72,14:0.17:86:43,10:29,4:65,7,13,1
chr8 38133793 . G A . PASS AS_SB_TABLE=350,303|54,40;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=756;AS_FilterStatus=SITE;MBQ=38,38;MFRL=166,178;MMQ=60,60;MPOS=20;POPAF=0.688;TLOD=258.89 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:653,94:0.128:747:383,55:206,33:350,303,54,40
chr8 38143540 . G T . PASS AS_SB_TABLE=439,262|56,33;ECNT=2;GERMQ=93;SOURCES=mutect2;DP=829;AS_FilterStatus=SITE;MBQ=38,38;MFRL=151,163;MMQ=60,60;MPOS=21;POPAF=0.672;TLOD=235.71 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:701,89:0.119:790:294,37:302,42:439,262,56,33
chr8 38143572 . T G . PASS AS_SB_TABLE=377,385|47,53;ECNT=2;GERMQ=93;SOURCES=mutect2;DP=907;AS_FilterStatus=SITE;MBQ=38,38;MFRL=150,160;MMQ=60,60;MPOS=15;POPAF=0.672;TLOD=259.37 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:762,100:0.116:862:272,34:275,36:377,385,47,53
chr8 38149404 . C T . PASS AS_SB_TABLE=45,80|4,7;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=143;AS_FilterStatus=SITE;MBQ=38,38;MFRL=181,202;MMQ=60,60;MPOS=16;POPAF=0.688;TLOD=28.98 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:125,11:0.089:136:67,6:50,5:45,80,4,7
chr8 38161469 . T C . PASS AS_SB_TABLE=170,48|36,13;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=275;AS_FilterStatus=SITE;MBQ=38,38;MFRL=176,172;MMQ=60,60;MPOS=15;POPAF=0.67;TLOD=143.33 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:218,49:0.184:267:123,30:83,16:170,48,36,13
chr8 38176109 . C T 0 LowFisherScore SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=15;SB=8.55967;SOURCES=mutect2,lancet GT:AD:SR:SA:DP 0/1:105,11:99,6:9,2:116
chr8 38176187 . T G 0 LowFisherScore SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=15;SB=13.1646;SOURCES=mutect2,lancet GT:AD:SR:SA:DP 0/1:114,26:59,55:18,8:140
chr8 38176435 . T G 0 LowFisherScore;StrandBias SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=15;SB=0;SOURCES=lancet GT:AD:SR:SA:DP 0/1:12,4:0,12:0,4:16
chr8 38212586 MantaBND:53:0:1:0:0:0:1 C C]chr14:41598754] . . SVTYPE=BND;MATEID=MantaBND:53:0:1:0:0:0:0;CIPOS=0,4;HOMLEN=4;HOMSEQ=CAAC;BND_PAIR_COUNT=1;PAIR_COUNT=1 . .
chr8 38232738 . G T . PASS AS_SB_TABLE=13,25|2,2;ECNT=1;GERMQ=35;SOURCES=mutect2;DP=43;AS_FilterStatus=SITE;MBQ=38,38;MFRL=183,165;MMQ=60,60;MPOS=16;POPAF=0.672;TLOD=10.53 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:38,4:0.119:42:17,1:18,3:13,25,2,2
chr8 38243865 . T G . PASS AS_SB_TABLE=365,394|46,63;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=897;AS_FilterStatus=SITE;MBQ=38,38;MFRL=166,175;MMQ=60,60;MPOS=21;POPAF=0.67;TLOD=292.57 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:759,109:0.126:868:400,55:263,40:365,394,46,63
chr8 38258154 . G A . PASS AS_SB_TABLE=116,9|12,0;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=146;AS_FilterStatus=SITE;MBQ=38,38;MFRL=193,211;MMQ=60,60;MPOS=25;POPAF=0.69;TLOD=32.24 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:125,12:0.097:137:78,6:40,6:116,9,12,0
chr8 38259481 . T C . PASS AS_SB_TABLE=217,329|32,40;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=665;AS_FilterStatus=SITE;MBQ=38,38;MFRL=186,177;MMQ=60,60;MPOS=20;POPAF=0.666;TLOD=186.83 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:546,72:0.113:618:266,37:223,27:217,329,32,40
chr8 38262570 . C T . PASS AS_SB_TABLE=299,109|141,30;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=600;AS_FilterStatus=SITE;MBQ=38,38;MFRL=186,190;MMQ=60,60;MPOS=17;POPAF=7.3;TLOD=542.89 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:408,171:0.294:579:213,83:182,80:299,109,141,30
chr8 38268418 . T C . PASS AS_SB_TABLE=259,469|43,76;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=913;AS_FilterStatus=SITE;MBQ=38,38;MFRL=190,200;MMQ=60,60;MPOS=17;POPAF=3.29;TLOD=337.39 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:728,119:0.143:847:398,70:276,43:259,469,43,76
chr8 38268524 . A G . PASS AS_SB_TABLE=272,338|17,36;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=706;AS_FilterStatus=SITE;MBQ=38,38;MFRL=207,204;MMQ=60,60;MPOS=24;POPAF=7.3;TLOD=137.03 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:610,53:0.082:663:295,28:273,22:272,338,17,36
chr8 38269514 . T C . PASS AS_SB_TABLE=209,296|25,45;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=601;AS_FilterStatus=SITE;MBQ=38,38;MFRL=164,165;MMQ=60,60;MPOS=18;POPAF=0.666;TLOD=184.74 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:505,70:0.121:575:275,37:194,28:209,296,25,45
chr8 38271209 . G A . PASS AS_SB_TABLE=910,537|90,60;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=1668;AS_FilterStatus=SITE;MBQ=38,38;MFRL=173,172;MMQ=60,60;MPOS=17;POPAF=4.31;TLOD=395.71 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:1447,150:0.097:1597:686,76:632,65:910,537,90,60
chr8 38271287 MantaBND:351:0:1:0:0:0:1 G ]chr14:101504815]G . . SVTYPE=BND;MATEID=MantaBND:351:0:1:0:0:0:0;CIPOS=0,2;HOMLEN=2;HOMSEQ=TA;BND_PAIR_COUNT=1;PAIR_COUNT=1 . .
chr8 38271765 . G A 0 LowFisherScore SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=13;SB=13.4027;SOURCES=mutect2,lancet GT:AD:SR:SA:DP 0/1:1211,76:485,726:25,51:1287
chr8 38271849 . G A 0 LowFisherScore SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=13;SB=11.0151;SOURCES=mutect2,lancet GT:AD:SR:SA:DP 0/1:670,108:238,432:36,72:778
chr8 38272102 . G C . base_qual;clustered_events;strand_bias AS_SB_TABLE=867,639|14,0;ECNT=9;GERMQ=93;SOURCES=mutect2;DP=1599;AS_FilterStatus=base_qual;MBQ=38,11;MFRL=175,251;MMQ=60,60;MPOS=17;POPAF=7.3;TLOD=9.58 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:1506,14:0.007244:1520:663,0:490,1:867,639,14,0
chr8 38272106 . A G . base_qual;clustered_events;strand_bias AS_SB_TABLE=843,660|17,0;ECNT=9;GERMQ=93;SOURCES=mutect2;DP=1610;AS_FilterStatus=base_qual;MBQ=38,10;MFRL=172,324;MMQ=60,60;MPOS=17;POPAF=7.3;TLOD=8.31 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:1503,17:0.008587:1520:657,0:445,1:843,660,17,0
chr8 38272111 . A C . base_qual;clustered_events;strand_bias AS_SB_TABLE=801,678|14,0;ECNT=9;GERMQ=93;SOURCES=mutect2;DP=2032;AS_FilterStatus=base_qual;MBQ=38,11;MFRL=171,225;MMQ=60,60;MPOS=28;POPAF=7.3;TLOD=6.14 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:1479,14:0.006405:1493:629,0:424,0:801,678,14,0
chr8 38272115 . C A . base_qual;clustered_events;strand_bias AS_SB_TABLE=793,706|18,0;ECNT=9;GERMQ=93;SOURCES=mutect2;DP=1778;AS_FilterStatus=base_qual;MBQ=38,11;MFRL=170,241;MMQ=60,60;MPOS=24;POPAF=7.3;TLOD=4.13 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:1499,18:0.005264:1517:628,0:439,2:793,706,18,0
chr8 38272118 . G A . base_qual;clustered_events AS_SB_TABLE=783,726|14,3;ECNT=9;GERMQ=93;SOURCES=mutect2;DP=1779;AS_FilterStatus=base_qual;MBQ=38,11;MFRL=171,249;MMQ=60,60;MPOS=28;POPAF=7.3;TLOD=16.97 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:1509,17:0.01:1526:614,2:425,1:783,726,14,3
chr8 38274930 . G A . PASS AS_SB_TABLE=598,750|59,71;ECNT=2;GERMQ=93;SOURCES=mutect2;DP=1575;AS_FilterStatus=SITE;MBQ=38,38;MFRL=169,176;MMQ=60,60;MPOS=21;POPAF=4.13;TLOD=343.63 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:1348,130:0.092:1478:643,78:551,37:598,750,59,71
chr8 38275014 . G C . PASS AS_SB_TABLE=179,683|25,87;ECNT=2;GERMQ=93;SOURCES=mutect2;DP=1030;AS_FilterStatus=SITE;MBQ=38,38;MFRL=179,164;MMQ=60,60;MPOS=16;POPAF=3.49;TLOD=296.44 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:862,112:0.114:974:285,38:204,26:179,683,25,87
chr8 38275434 . C A . PASS AS_SB_TABLE=601,585|344,296;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=1865;AS_FilterStatus=SITE;MBQ=38,38;MFRL=167,182;MMQ=60,60;MPOS=20;POPAF=7.3;TLOD=2069.96 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:1186,640:0.354:1826:553,302:506,271:601,585,344,296
chr8 38276794 . CA C 0 LowFisherScore SOMATIC;FETS=0;TYPE=del;LEN=1;KMERSIZE=15;SB=19.7148;SOURCES=lancet GT:AD:SR:SA:DP 0/1:1552,602:830,722:345,257:2154
chr8 38277678 . C T . PASS AS_SB_TABLE=936,778|123,112;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=2066;AS_FilterStatus=SITE;MBQ=38,38;MFRL=194,199;MMQ=60,60;MPOS=18;POPAF=4.61;TLOD=649.13 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:1714,235:0.121:1949:870,123:729,97:936,778,123,112
chr8 38279248 . G A 1.4422 LowFisherScore SOMATIC;FETS=1.4422;TYPE=snv;LEN=1;KMERSIZE=13;SB=23.7804;SOURCES=mutect2,lancet GT:AD:SR:SA:DP 0/1:2047,370:997,1050:203,167:2417
chr8 38279259 . TC T 0.88475 LowFisherScore SOMATIC;FETS=0.88475;TYPE=del;LEN=1;KMERSIZE=13;SB=13.8289;SOURCES=lancet GT:AD:SR:SA:DP 0/1:2274,244:1090,1184:111,133:2518
chr8 38279368 . G A 1.69361 LowFisherScore SOMATIC;FETS=1.69361;TYPE=snv;LEN=1;KMERSIZE=13;SB=12.5835;SOURCES=mutect2,lancet GT:AD:SR:SA:DP 0/1:2224,228:1159,1065:118,110:2452
chr8 38279641 . G A 4.90487 LowFisherScore SOMATIC;FETS=4.90487;TYPE=snv;LEN=1;KMERSIZE=13;SB=23.2292;SOURCES=mutect2,lancet GT:AD:SR:SA:DP 0/1:1339,613:672,667:277,336:1952
chr8 38279738 MantaBND:21:1:14:0:3:0:0 G ]chr16:31142247]G . . SVTYPE=BND;MATEID=MantaBND:21:1:14:0:3:0:1;CIPOS=0,8;HOMLEN=8;HOMSEQ=GGCGGTGA;BND_PAIR_COUNT=1;PAIR_COUNT=1 . .
chr8 38279773 . G A 0 LowFisherScore SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=13;SB=12.2996;SOURCES=mutect2,lancet GT:AD:SR:SA:DP 0/1:1096,118:587,509:59,59:1214
chr8 38279977 . T C . PASS AS_SB_TABLE=175,828|39,128;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=1276;AS_FilterStatus=SITE;MBQ=38,38;MFRL=191,190;MMQ=60,60;MPOS=18;POPAF=2.04;TLOD=464.61 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:1003,167:0.141:1170:489,88:441,66:175,828,39,128
chr8 38280636 . C T 0.427386 LowFisherScore SOMATIC;FETS=0.427386;TYPE=snv;LEN=1;KMERSIZE=25;SB=11.1207;SOURCES=mutect2,lancet GT:AD:SR:SA:DP 0/1:1664,84:822,842:44,40:1748
chr8 38280673 . C T 1.90503 LowFisherScore SOMATIC;FETS=1.90503;TYPE=snv;LEN=1;KMERSIZE=25;SB=13.5335;SOURCES=mutect2,lancet GT:AD:SR:SA:DP 0/1:1643,259:839,804:127,132:1902
chr8 38280830 MantaDEL:348:0:0:3:0:0 GTTTTTTTTT G . . END=38280839;SVTYPE=DEL;SVLEN=-9;CIPOS=0,14;HOMLEN=14;HOMSEQ=TTTTTTTTTTTTTT;UPSTREAM_PAIR_COUNT=0;DOWNSTREAM_PAIR_COUNT=0;PAIR_COUNT=0;CIGAR=1M9D . .
chr8 38280836 . T A . clustered_events;strand_bias AS_SB_TABLE=98,1062|0,135;ECNT=4;GERMQ=93;SOURCES=mutect2;DP=1422;AS_FilterStatus=strand_bias;MBQ=38,38;MFRL=214,220;MMQ=60,60;MPOS=24;POPAF=7.3;TLOD=6.8 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:1160,135:0.077:1295:117,15:65,5:98,1062,0,135
chr8 38280837 . T A . clustered_events;strand_bias AS_SB_TABLE=84,1104|0,108;ECNT=4;GERMQ=93;SOURCES=mutect2;DP=1409;AS_FilterStatus=strand_bias;MBQ=38,37;MFRL=217,206;MMQ=60,60;MPOS=23;POPAF=7.3;TLOD=33.06 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:1188,108:0.069:1296:142,13:98,14:84,1104,0,108
chr8 38280838 . T A . clustered_events;strand_bias AS_SB_TABLE=76,1179|0,51;ECNT=4;GERMQ=93;SOURCES=mutect2;DP=1403;AS_FilterStatus=strand_bias;MBQ=38,38;MFRL=217,207;MMQ=60,60;MPOS=22;POPAF=7.3;TLOD=21.27 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:1255,51:0.033:1306:200,10:153,13:76,1179,0,51
chr8 38281180 MantaDEL:50:1:1:2:8:0 TAAAAAAAAA T . . END=38281189;SVTYPE=DEL;SVLEN=-9;CIPOS=0,12;HOMLEN=12;HOMSEQ=AAAAAAAAAAAA;UPSTREAM_PAIR_COUNT=0;DOWNSTREAM_PAIR_COUNT=0;PAIR_COUNT=0;CIGAR=1M9D . .
chr8 38281180 MantaDEL:50:1:1:3:4:0 TAAAAAAAAA T . . END=38281189;SVTYPE=DEL;SVLEN=-9;CIPOS=0,12;HOMLEN=12;HOMSEQ=AAAAAAAAAAAA;UPSTREAM_PAIR_COUNT=0;DOWNSTREAM_PAIR_COUNT=0;PAIR_COUNT=0;CIGAR=1M9D . .
chr8 38282226 MantaBND:50:1:8:0:1:0:1 G [chr19:43099447[G . . SVTYPE=BND;MATEID=MantaBND:50:1:8:0:1:0:0;CIPOS=0,11;HOMLEN=11;HOMSEQ=ATGGGAGAGGA;BND_PAIR_COUNT=1;PAIR_COUNT=1 . .
chr8 38282317 . T C 0.631273 LowFisherScore SOMATIC;FETS=0.631273;TYPE=snv;LEN=1;KMERSIZE=17;SB=17.9018;SOURCES=mutect2,lancet GT:AD:SR:SA:DP 0/1:1723,130:944,779:61,69:1853
chr8 38283597 MantaBND:125:0:1:0:1:0:0 C ]chr3:131688894]C . . SVTYPE=BND;MATEID=MantaBND:125:0:1:0:1:0:1;CIPOS=0,6;HOMLEN=6;HOMSEQ=TTCCCA;BND_PAIR_COUNT=1;PAIR_COUNT=1 . .
chr8 38283620 . T C . PASS AS_SB_TABLE=990,859|155,160;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=2299;AS_FilterStatus=SITE;MBQ=38,38;MFRL=182,186;MMQ=60,60;MPOS=18;POPAF=4.31;TLOD=880.41 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:1849,315:0.147:2164:869,147:818,149:990,859,155,160
chr8 38284357 . G A 0.0269917 LowFisherScore;LowVafTumor;StrandBias SOMATIC;FETS=0.0269917;TYPE=snv;LEN=1;KMERSIZE=25;SB=0.189887;SOURCES=lancet GT:AD:SR:SA:DP 0/1:801,5:7,794:0,5:806
chr8 38284641 . G A 8.45098 LowCovNormal SOMATIC;FETS=8.45098;TYPE=snv;LEN=1;KMERSIZE=17;SB=0.347621;SOURCES=mutect2,lancet GT:AD:SR:SA:DP 0/1:1,12:1,0:11,1:13
chr8 38284700 . TA T 0.493028 LowFisherScore SOMATIC;FETS=0.493028;TYPE=del;LEN=1;KMERSIZE=17;SB=9.56341;SOURCES=lancet GT:AD:SR:SA:DP 0/1:182,22:119,63:12,10:204
chr8 38285007 . A G 0 LowFisherScore;StrandBias SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=15;SB=2.26301;SOURCES=lancet GT:AD:SR:SA:DP 0/1:67,3:56,11:3,0:70
chr8 38285314 . T A . PASS AS_SB_TABLE=496,183|30,18;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=780;AS_FilterStatus=SITE;MBQ=38,38;MFRL=271,271;MMQ=60,60;MPOS=15;POPAF=7.3;TLOD=118.34 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:679,48:0.067:727:371,30:302,17:496,183,30,18
chr8 38285611 . G A 0.869642 LowFisherScore SOMATIC;FETS=0.869642;TYPE=snv;LEN=1;KMERSIZE=23;SB=11.202;SOURCES=mutect2,lancet GT:AD:SR:SA:DP 0/1:1722,119:771,951:53,66:1841
chr8 38286225 . G A 5.38149 LowCovNormal;HighVafNormal;HighAltCntNormal SHARED;FETS=5.38149;TYPE=snv;LEN=1;KMERSIZE=15;SB=20.8776;SOURCES=mutect2,lancet GT:AD:SR:SA:DP 0/1:1370,1055:743,627:608,447:2425
chr8 38286811 . C G 3.07855 LowFisherScore SOMATIC;FETS=3.07855;TYPE=snv;LEN=1;KMERSIZE=13;SB=12.9412;SOURCES=mutect2,lancet GT:AD:SR:SA:DP 0/1:1855,283:947,908:145,138:2138
chr8 38287108 . AG A 2.98956 LowFisherScore SOMATIC;FETS=2.98956;TYPE=del;LEN=1;KMERSIZE=13;SB=14.4139;SOURCES=lancet GT:AD:SR:SA:DP 0/1:1622,667:789,833:327,340:2289
chr8 38287144 . A G . base_qual;clustered_events;strand_bias AS_SB_TABLE=971,860|0,53;ECNT=3;GERMQ=93;SOURCES=mutect2;DP=2012;AS_FilterStatus=base_qual;MBQ=38,11;MFRL=177,157;MMQ=60,60;MPOS=17;POPAF=7.3;TLOD=3.44 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:1831,53:0.0078:1884:709,8:573,0:971,860,0,53
chr8 38287154 . A G . clustered_events;strand_bias AS_SB_TABLE=951,792|1,80;ECNT=3;GERMQ=93;SOURCES=mutect2;DP=1992;AS_FilterStatus=strand_bias;MBQ=37,22;MFRL=178,148;MMQ=60,60;MPOS=19;POPAF=7.3;TLOD=31.87 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:1743,81:0.023:1824:691,4:530,8:951,792,1,80
chr8 38289085 . G T . PASS AS_SB_TABLE=412,511|24,44;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=1057;AS_FilterStatus=SITE;MBQ=38,38;MFRL=174,162;MMQ=60,60;MPOS=19;POPAF=7.3;TLOD=168.54 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:923,68:0.069:991:480,34:348,29:412,511,24,44
chr8 38299715 . G C . PASS AS_SB_TABLE=281,317|42,44;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=697;AS_FilterStatus=SITE;MBQ=38,38;MFRL=169,168;MMQ=60,60;MPOS=22;POPAF=0.357;TLOD=239.29 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:598,86:0.13:684:323,43:212,37:281,317,42,44
chr8 38299880 MantaDEL:350:0:0:0:1:0 GGTGTGTGT G . . END=38299888;SVTYPE=DEL;SVLEN=-8;CIPOS=0,25;HOMLEN=25;HOMSEQ=GTGTGTGTGTGTGTGTGTGTGTGTG;UPSTREAM_PAIR_COUNT=0;DOWNSTREAM_PAIR_COUNT=0;PAIR_COUNT=0;CIGAR=1M8D . .
chr8 38302965 . C T . PASS AS_SB_TABLE=61,107|17,12;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=216;AS_FilterStatus=SITE;MBQ=38,38;MFRL=179,168;MMQ=60,60;MPOS=27;POPAF=0.635;TLOD=83.24 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:168,29:0.153:197:99,17:59,11:61,107,17,12
chr8 38311001 . C T . germline AS_SB_TABLE=113,79|85,34;ECNT=1;GERMQ=1;SOURCES=mutect2;DP=329;AS_FilterStatus=SITE;MBQ=38,38;MFRL=170,170;MMQ=60,60;MPOS=16;POPAF=0.411;TLOD=399.29 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:192,119:0.393:311:103,66:71,47:113,79,85,34
chr8 38318337 . G C . germline AS_SB_TABLE=106,67|151,85;ECNT=1;GERMQ=1;SOURCES=mutect2;DP=427;AS_FilterStatus=SITE;MBQ=38,38;MFRL=166,165;MMQ=60,60;MPOS=16;POPAF=0.352;TLOD=780.35 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:173,236:0.582:409:88,108:57,96:106,67,151,85
chr8 38322346 . A G . germline AS_SB_TABLE=0,0|183,26;ECNT=1;GERMQ=1;SOURCES=mutect2;DP=212;AS_FilterStatus=SITE;MBQ=0,38;MFRL=0,224;MMQ=60,60;MPOS=19;POPAF=0.211;TLOD=857.05 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:0,209:0.995:209:0,99:0,102:0,0,183,26
chr8 38322620 . G A . PASS AS_SB_TABLE=46,221|28,145;ECNT=1;GERMQ=3;SOURCES=mutect2;DP=460;AS_FilterStatus=SITE;MBQ=38,38;MFRL=185,177;MMQ=60,60;MPOS=21;POPAF=1.08;TLOD=543.74 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:267,173:0.393:440:126,89:113,63:46,221,28,145
chr8 38328302 . A G . germline AS_SB_TABLE=245,159|302,201;ECNT=1;GERMQ=1;SOURCES=mutect2;DP=974;AS_FilterStatus=SITE;MBQ=38,38;MFRL=171,165;MMQ=60,60;MPOS=19;POPAF=0.438;TLOD=1694.79 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:404,503:0.557:907:200,248:159,193:245,159,302,201
chr8 38331827 . G C . germline AS_SB_TABLE=0,0|12,217;ECNT=1;GERMQ=1;SOURCES=mutect2;DP=249;AS_FilterStatus=SITE;MBQ=0,38;MFRL=0,223;MMQ=60,60;MPOS=16;POPAF=0.007005;TLOD=940.99 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:0,229:0.996:229:0,131:0,89:0,0,12,217
chr8 38366249 . C T . PASS AS_SB_TABLE=43,57|204,368;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=682;AS_FilterStatus=SITE;MBQ=38,38;MFRL=172,167;MMQ=60,60;MPOS=15;POPAF=0.249;TLOD=2043.74 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:100,572:0.849:672:59,298:26,181:43,57,204,368
chr8 38377057 . G A . PASS AS_SB_TABLE=26,13|91,25;ECNT=1;GERMQ=34;SOURCES=mutect2;DP=192;AS_FilterStatus=SITE;MBQ=38,38;MFRL=177,184;MMQ=60,60;MPOS=27;POPAF=0.164;TLOD=435.95 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:39,116:0.752:155:18,61:9,32:26,13,91,25
chr8 38385389 . T A . PASS AS_SB_TABLE=78,3|363,26;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=494;AS_FilterStatus=SITE;MBQ=38,38;MFRL=196,194;MMQ=60,60;MPOS=16;POPAF=0.138;TLOD=1464.62 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:81,389:0.82:470:40,210:41,154:78,3,363,26
chr8 38385486 . G A . PASS AS_SB_TABLE=47,61|419,292;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=851;AS_FilterStatus=SITE;MBQ=38,38;MFRL=179,174;MMQ=60,60;MPOS=14;POPAF=0.164;TLOD=2688.66 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:108,711:0.864:819:46,339:57,313:47,61,419,292
chr8 38401296 . T G . PASS AS_SB_TABLE=69,77|307,472;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=952;AS_FilterStatus=SITE;MBQ=38,38;MFRL=180,168;MMQ=60,60;MPOS=20;POPAF=0.164;TLOD=2874.98 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:146,779:0.842:925:77,396:49,273:69,77,307,472
chr8 38417673 . C T . PASS AS_SB_TABLE=35,3|137,49;ECNT=2;GERMQ=93;SOURCES=mutect2;DP=231;AS_FilterStatus=SITE;MBQ=38,38;MFRL=171,158;MMQ=60,60;MPOS=21;POPAF=0.177;TLOD=653.52 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:38,186:0.812:224:21,86:16,72:35,3,137,49
chr8 38417736 . C A . PASS AS_SB_TABLE=13,20|102,101;ECNT=2;GERMQ=93;SOURCES=mutect2;DP=256;AS_FilterStatus=SITE;MBQ=38,38;MFRL=158,158;MMQ=60,60;MPOS=19;POPAF=0.174;TLOD=770.6 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:33,203:0.861:236:10,75:8,59:13,20,102,101
chr8 38426012 . A G . PASS AS_SB_TABLE=27,33|149,255;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=478;AS_FilterStatus=SITE;MBQ=38,38;MFRL=161,174;MMQ=60,60;MPOS=19;POPAF=0.282;TLOD=1519.89 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:60,404:0.876:464:26,220:25,147:27,33,149,255
chr8 38440657 . G A . PASS AS_SB_TABLE=303,157|37,19;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=522;AS_FilterStatus=SITE;MBQ=38,38;MFRL=172,176;MMQ=60,60;MPOS=23;POPAF=0.52;TLOD=149.45 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:460,56:0.111:516:240,35:186,17:303,157,37,19
chr8 38447248 . A G . germline AS_SB_TABLE=0,0|77,173;ECNT=2;GERMQ=1;SOURCES=mutect2;DP=262;AS_FilterStatus=SITE;MBQ=0,38;MFRL=0,174;MMQ=60,60;MPOS=16;POPAF=0.099;TLOD=997.22 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:0,250:0.996:250:0,127:0,107:0,0,77,173
chr8 38447263 . A G . germline AS_SB_TABLE=0,0|59,140;ECNT=2;GERMQ=1;SOURCES=mutect2;DP=223;AS_FilterStatus=SITE;MBQ=0,38;MFRL=0,182;MMQ=60,60;MPOS=15;POPAF=0.001305;TLOD=801.6 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:0,199:0.995:199:0,100:0,75:0,0,59,140
chr8 38460773 . C T . PASS AS_SB_TABLE=44,49|207,300;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=636;AS_FilterStatus=SITE;MBQ=38,38;MFRL=192,182;MMQ=60,60;MPOS=15;POPAF=0.165;TLOD=1974.77 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:93,507:0.845:600:45,276:42,203:44,49,207,300
chr8 38481152 . G C . base_qual;clustered_events;strand_bias AS_SB_TABLE=327,211|28,0;ECNT=6;GERMQ=93;SOURCES=mutect2;DP=601;AS_FilterStatus=base_qual;MBQ=34,10;MFRL=168,164;MMQ=60,60;MPOS=27;POPAF=7.3;TLOD=6.79 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:538,28:0.017:566:164,5:152,1:327,211,28,0
chr8 38481157 . A C . clustered_events;strand_bias AS_SB_TABLE=316,228|22,0;ECNT=6;GERMQ=93;SOURCES=mutect2;DP=620;AS_FilterStatus=strand_bias;MBQ=37,22;MFRL=166,143;MMQ=60,60;MPOS=29;POPAF=7.3;TLOD=6.35 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:544,22:0.016:566:161,8:143,0:316,228,22,0
chr8 38481160 . A C . base_qual;clustered_events;strand_bias AS_SB_TABLE=321,233|26,0;ECNT=6;GERMQ=93;SOURCES=mutect2;DP=614;AS_FilterStatus=base_qual;MBQ=37,11;MFRL=167,135;MMQ=60,60;MPOS=25;POPAF=7.3;TLOD=3.24 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:554,26:0.016:580:166,3:157,2:321,233,26,0
chr8 38481163 . G C . base_qual;clustered_events;strand_bias AS_SB_TABLE=322,259|15,0;ECNT=6;GERMQ=93;SOURCES=mutect2;DP=621;AS_FilterStatus=base_qual;MBQ=37,11;MFRL=166,170;MMQ=60,60;MPOS=24;POPAF=7.3;TLOD=3.49 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:581,15:0.012:596:127,1:132,0:322,259,15,0
chr8 38481169 . T C . base_qual;clustered_events;strand_bias AS_SB_TABLE=301,270|30,0;ECNT=6;GERMQ=93;SOURCES=mutect2;DP=634;AS_FilterStatus=base_qual;MBQ=36,11;MFRL=165,144;MMQ=60,60;MPOS=20;POPAF=7.3;TLOD=7.27 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:571,30:0.02:601:145,1:130,2:301,270,30,0
chr8 38481183 . C T . clustered_events AS_SB_TABLE=368,276|23,20;ECNT=6;GERMQ=93;SOURCES=mutect2;DP=703;AS_FilterStatus=SITE;MBQ=38,38;MFRL=161,170;MMQ=60,60;MPOS=22;POPAF=0.441;TLOD=99.58 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:644,43:0.063:687:240,9:177,17:368,276,23,20
chr8 38486970 . G A . germline AS_SB_TABLE=55,136|59,128;ECNT=1;GERMQ=1;SOURCES=mutect2;DP=400;AS_FilterStatus=SITE;MBQ=38,38;MFRL=188,192;MMQ=60,60;MPOS=17;POPAF=0.333;TLOD=645.26 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:191,187:0.489:378:98,101:84,75:55,136,59,128
chr8 38498637 . C T . PASS AS_SB_TABLE=133,84|247,185;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=698;AS_FilterStatus=SITE;MBQ=38,38;MFRL=164,173;MMQ=60,60;MPOS=20;POPAF=0.131;TLOD=1612.96 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:217,432:0.669:649:116,232:83,179:133,84,247,185
chr8 38508987 . T A . PASS AS_SB_TABLE=73,64|143,137;ECNT=2;GERMQ=52;SOURCES=mutect2;DP=433;AS_FilterStatus=SITE;MBQ=38,38;MFRL=156,167;MMQ=60,60;MPOS=20;POPAF=0.127;TLOD=994.1 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:137,280:0.674:417:66,154:56,95:73,64,143,137
chr8 38509005 . C T . PASS AS_SB_TABLE=174,177|42,44;ECNT=2;GERMQ=93;SOURCES=mutect2;DP=442;AS_FilterStatus=SITE;MBQ=38,38;MFRL=157,168;MMQ=60,60;MPOS=21;POPAF=0.395;TLOD=235.49 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:351,86:0.196:437:177,43:115,26:174,177,42,44
chr8 38514745 . C A . PASS AS_SB_TABLE=100,105|24,37;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=288;AS_FilterStatus=SITE;MBQ=38,38;MFRL=182,189;MMQ=60,60;MPOS=16;POPAF=0.391;TLOD=183.3 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:205,61:0.234:266:112,33:74,22:100,105,24,37
chr8 110223389 MantaBND:158:0:1:0:1:0:1 C [chr4:25676115[C . . SVTYPE=BND;MATEID=MantaBND:158:0:1:0:1:0:0;CIPOS=0,6;HOMLEN=6;HOMSEQ=AAAACC;BND_PAIR_COUNT=1;PAIR_COUNT=1 . .
chr8 128550123 . A G . germline AS_SB_TABLE=110,40|147,31;ECNT=1;GERMQ=1;SOURCES=mutect2;DP=352;AS_FilterStatus=SITE;MBQ=38,38;MFRL=188,204;MMQ=60,60;MPOS=20;POPAF=0.234;TLOD=642.23 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:150,178:0.549:328:77,97:64,76:110,40,147,31
chr8 128568737 . G T . PASS AS_SB_TABLE=160,7|50,0;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=239;AS_FilterStatus=SITE;MBQ=38,38;MFRL=197,206;MMQ=60,60;MPOS=17;POPAF=0.943;TLOD=155.66 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:167,50:0.235:217:83,28:81,22:160,7,50,0
chr8 128568856 . G A . PASS AS_SB_TABLE=168,217|21,21;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=447;AS_FilterStatus=SITE;MBQ=38,38;MFRL=162,185;MMQ=60,60;MPOS=20;POPAF=0.561;TLOD=111.49 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:385,42:0.106:427:209,25:132,14:168,217,21,21
chr8 128581326 . T C . PASS AS_SB_TABLE=330,111|81,34;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=590;AS_FilterStatus=SITE;MBQ=38,38;MFRL=180,179;MMQ=60,60;MPOS=19;POPAF=0.53;TLOD=335.44 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:441,115:0.21:556:231,65:165,40:330,111,81,34
chr8 128581444 . T G . germline AS_SB_TABLE=31,258|23,185;ECNT=1;GERMQ=1;SOURCES=mutect2;DP=530;AS_FilterStatus=SITE;MBQ=38,38;MFRL=193,179;MMQ=60,60;MPOS=20;POPAF=0.165;TLOD=678.44 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:289,208:0.41:497:158,103:102,73:31,258,23,185
chr8 128590946 . A G . PASS AS_SB_TABLE=368,368|50,36;ECNT=2;GERMQ=93;SOURCES=mutect2;DP=842;AS_FilterStatus=SITE;MBQ=38,38;MFRL=171,174;MMQ=60,60;MPOS=13;POPAF=0.721;TLOD=232.63 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:736,86:0.11:822:375,47:274,35:368,368,50,36
chr8 128590962 . C T . PASS AS_SB_TABLE=301,335|92,112;ECNT=2;GERMQ=93;SOURCES=mutect2;DP=884;AS_FilterStatus=SITE;MBQ=38,38;MFRL=166,174;MMQ=60,60;MPOS=17;POPAF=0.818;TLOD=615.59 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:636,204:0.245:840:317,102:216,77:301,335,92,112
chr8 128591290 MantaDEL:361:0:0:0:1:0 CATTTTTTTTTTTTTTTTTTTTTT C . . END=128591313;SVTYPE=DEL;SVLEN=-23;UPSTREAM_PAIR_COUNT=0;DOWNSTREAM_PAIR_COUNT=0;PAIR_COUNT=0;CIGAR=1M23D . .
chr8 128599908 . C T . PASS AS_SB_TABLE=286,293|118,104;ECNT=2;GERMQ=93;SOURCES=mutect2;DP=822;AS_FilterStatus=SITE;MBQ=38,38;MFRL=173,167;MMQ=60,60;MPOS=15;POPAF=0.827;TLOD=676.08 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:579,222:0.279:801:277,94:239,104:286,293,118,104
chr8 128599944 . G A . PASS AS_SB_TABLE=319,405|36,56;ECNT=2;GERMQ=93;SOURCES=mutect2;DP=828;AS_FilterStatus=SITE;MBQ=38,38;MFRL=170,184;MMQ=60,60;MPOS=19;POPAF=0.346;TLOD=250.47 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:724,92:0.114:816:303,31:279,45:319,405,36,56
chr8 128606603 . A G . germline AS_SB_TABLE=189,115|136,73;ECNT=1;GERMQ=1;SOURCES=mutect2;DP=524;AS_FilterStatus=SITE;MBQ=38,38;MFRL=166,177;MMQ=60,60;MPOS=18;POPAF=0.267;TLOD=710.55 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:304,209:0.417:513:169,119:105,77:189,115,136,73
chr8 128617484 . G A . clustered_events AS_SB_TABLE=366,296|200,145;ECNT=5;GERMQ=93;SOURCES=mutect2;DP=1064;AS_FilterStatus=SITE;MBQ=38,38;MFRL=164,171;MMQ=60,60;MPOS=18;POPAF=0.58;TLOD=1085.47 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:662,345:0.346:1007:301,157:264,146:366,296,200,145
chr8 128617505 . T C . clustered_events AS_SB_TABLE=463,464|51,54;ECNT=5;GERMQ=93;SOURCES=mutect2;DP=1107;AS_FilterStatus=SITE;MBQ=38,38;MFRL=164,184;MMQ=60,60;MPOS=19;POPAF=3.29;TLOD=285.57 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:927,105:0.108:1032:399,45:324,48:463,464,51,54
chr8 128617522 . A G . clustered_events AS_SB_TABLE=388,522|47,81;ECNT=5;GERMQ=93;SOURCES=mutect2;DP=1084;AS_FilterStatus=SITE;MBQ=38,38;MFRL=165,172;MMQ=60,60;MPOS=19;POPAF=0.597;TLOD=351.71 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:910,128:0.126:1038:354,52:307,36:388,522,47,81
chr8 128617544 . C T . clustered_events AS_SB_TABLE=64,125|251,523;ECNT=5;GERMQ=93;SOURCES=mutect2;DP=988;AS_FilterStatus=SITE;MBQ=38,38;MFRL=161,166;MMQ=60,60;MPOS=19;POPAF=0.045;TLOD=2841.34 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:189,774:0.807:963:66,258:49,218:64,125,251,523
chr8 128617612 . T C . clustered_events AS_SB_TABLE=46,409|4,41;ECNT=5;GERMQ=93;SOURCES=mutect2;DP=505;AS_FilterStatus=SITE;MBQ=38,38;MFRL=199,194;MMQ=60,60;MPOS=20;POPAF=0.431;TLOD=119.79 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:455,45:0.093:500:89,9:70,4:46,409,4,41
chr8 128625257 . A G . PASS AS_SB_TABLE=210,10|99,3;ECNT=2;GERMQ=51;SOURCES=mutect2;DP=335;AS_FilterStatus=SITE;MBQ=38,38;MFRL=185,184;MMQ=60,60;MPOS=15;POPAF=0.326;TLOD=341.68 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:220,102:0.323:322:120,50:92,50:210,10,99,3
chr8 128625294 . T G . PASS AS_SB_TABLE=220,59|115,35;ECNT=2;GERMQ=37;SOURCES=mutect2;DP=453;AS_FilterStatus=SITE;MBQ=38,38;MFRL=171,170;MMQ=60,60;MPOS=24;POPAF=0.323;TLOD=461.1 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:279,150:0.343:429:124,62:104,60:220,59,115,35
chr8 128625389 . G C . PASS AS_SB_TABLE=62,149|24,72;ECNT=1;GERMQ=51;SOURCES=mutect2;DP=328;AS_FilterStatus=SITE;MBQ=38,38;MFRL=171,179;MMQ=60,60;MPOS=17;POPAF=0.327;TLOD=312.12 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:211,96:0.318:307:110,50:91,42:62,149,24,72
chr8 128631217 . A G . germline AS_SB_TABLE=52,61|37,32;ECNT=1;GERMQ=1;SOURCES=mutect2;DP=187;AS_FilterStatus=SITE;MBQ=38,38;MFRL=166,166;MMQ=60,60;MPOS=20;POPAF=0.465;TLOD=219.23 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:113,69:0.37:182:56,37:48,24:52,61,37,32
chr8 128637467 . A G . germline AS_SB_TABLE=79,131|89,150;ECNT=2;GERMQ=1;SOURCES=mutect2;DP=460;AS_FilterStatus=SITE;MBQ=38,38;MFRL=161,164;MMQ=60,60;MPOS=17;POPAF=0.27;TLOD=825.52 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:210,239:0.536:449:105,112:75,91:79,131,89,150
chr8 128637525 . G A . PASS AS_SB_TABLE=36,198|13,64;ECNT=2;GERMQ=93;SOURCES=mutect2;DP=323;AS_FilterStatus=SITE;MBQ=38,38;MFRL=171,189;MMQ=60,60;MPOS=13;POPAF=1.57;TLOD=247.91 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:234,77:0.259:311:63,25:63,25:36,198,13,64
chr8 128645587 . T C . PASS AS_SB_TABLE=61,1|12,0;ECNT=2;GERMQ=46;SOURCES=mutect2;DP=77;AS_FilterStatus=SITE;MBQ=38,38;MFRL=246,239;MMQ=60,60;MPOS=9;POPAF=0.928;TLOD=34.51 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:62,12:0.173:74:29,7:32,5:61,1,12,0
chr8 128645670 . C G . germline AS_SB_TABLE=155,7|158,5;ECNT=2;GERMQ=1;SOURCES=mutect2;DP=351;AS_FilterStatus=SITE;MBQ=38,38;MFRL=192,188;MMQ=60,60;MPOS=13;POPAF=0.418;TLOD=563.08 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:162,163:0.505:325:75,88:78,70:155,7,158,5
chr8 128653726 . T C . germline AS_SB_TABLE=164,108|224,161;ECNT=2;GERMQ=1;SOURCES=mutect2;DP=667;AS_FilterStatus=SITE;MBQ=38,38;MFRL=166,175;MMQ=60,60;MPOS=17;POPAF=0.247;TLOD=1360.28 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:272,385:0.591:657:145,196:104,165:164,108,224,161
chr8 128653743 . G A . PASS AS_SB_TABLE=385,322|35,34;ECNT=2;GERMQ=93;SOURCES=mutect2;DP=800;AS_FilterStatus=SITE;MBQ=38,38;MFRL=170,173;MMQ=60,60;MPOS=18;POPAF=2.8;TLOD=178.6 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:707,69:0.093:776:346,35:269,27:385,322,35,34
chr8 128663507 . G A . haplotype AS_SB_TABLE=73,113|17,53;ECNT=2;GERMQ=79;SOURCES=mutect2;DP=268;AS_FilterStatus=SITE;MBQ=38,38;MFRL=165,187;MMQ=60,60;MPOS=16;POPAF=0.79;TLOD=223.72 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:186,70:0.288:256:105,38:60,28:0|1:128663507_G_A:128663507:73,113,17,53
chr8 128663509 . A T . germline;haplotype AS_SB_TABLE=45,76|40,90;ECNT=2;GERMQ=1;SOURCES=mutect2;DP=268;AS_FilterStatus=SITE;MBQ=38,38;MFRL=160,177;MMQ=60,60;MPOS=16;POPAF=0.249;TLOD=479.79 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:121,130:0.534:251:68,72:37,45:0|1:128663507_G_A:128663507:45,76,40,90
chr8 128673107 . C T . PASS AS_SB_TABLE=225,290|96,98;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=735;AS_FilterStatus=SITE;MBQ=38,38;MFRL=168,175;MMQ=60,60;MPOS=16;POPAF=0.409;TLOD=591.31 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:515,194:0.281:709:257,100:180,72:225,290,96,98
chr8 128689613 . C A . PASS AS_SB_TABLE=204,107|114,25;ECNT=2;GERMQ=93;SOURCES=mutect2;DP=480;AS_FilterStatus=SITE;MBQ=38,38;MFRL=168,178;MMQ=60,60;MPOS=17;POPAF=0.684;TLOD=449.18 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:311,139:0.314:450:136,67:150,66:204,107,114,25
chr8 128689673 . G C . PASS AS_SB_TABLE=214,239|147,91;ECNT=2;GERMQ=93;SOURCES=mutect2;DP=744;AS_FilterStatus=SITE;MBQ=38,38;MFRL=168,157;MMQ=60,60;MPOS=19;POPAF=0.688;TLOD=733.75 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:453,238:0.341:691:177,106:148,74:214,239,147,91
chr8 128700175 . A G 0 LowFisherScore;LowAltCntTumor;StrandBias SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=13;SB=0;SOURCES=lancet GT:AD:SR:SA:DP 0/1:10,2:10,0:2,0:12
chr8 128700233 . T C 0 LowFisherScore;StrandBias SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=13;SB=0;SOURCES=lancet GT:AD:SR:SA:DP 0/1:7,17:7,0:17,0:24
chr8 128700344 . C T 0 LowFisherScore SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=13;SB=1.81695;SOURCES=lancet GT:AD:SR:SA:DP 0/1:40,77:40,0:76,1:117
chr8 128700384 . T C 0 LowFisherScore;StrandBias SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=13;SB=1.2078;SOURCES=lancet GT:AD:SR:SA:DP 0/1:215,32:213,2:32,0:247
chr8 128700392 . C T 0 LowFisherScore;LowVafTumor;LowAltCntTumor;StrandBias SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=13;SB=0.0756949;SOURCES=lancet GT:AD:SR:SA:DP 0/1:229,2:227,2:2,0:231
chr8 128700459 . C CA 0 LowFisherScore SOMATIC;FETS=0;TYPE=ins;LEN=1;KMERSIZE=13;SB=15.7105;SOURCES=lancet GT:AD:SR:SA:DP 0/1:209,364:145,64:273,91:573
chr8 128700545 . A G 0 LowFisherScore SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=15;SB=10.9051;SOURCES=mutect2,lancet GT:AD:SR:SA:DP 0/1:137,414:46,91:143,271:551
chr8 128700652 . G A 0 LowFisherScore SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=15;SB=12.5151;SOURCES=mutect2,lancet GT:AD:SR:SA:DP 0/1:69,231:11,58:22,209:300
chr8 128700656 . G A 0 LowFisherScore;LowVafTumor;LowAltCntTumor;StrandBias SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=15;SB=1.18976;SOURCES=lancet GT:AD:SR:SA:DP 0/1:61,2:8,53:0,2:63
chr8 128719884 . A T . PASS AS_SB_TABLE=111,302|20,60;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=501;AS_FilterStatus=SITE;MBQ=38,38;MFRL=167,162;MMQ=60,60;MPOS=16;POPAF=0.45;TLOD=226.6 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:413,80:0.164:493:205,36:155,31:111,302,20,60
chr8 128719982 . T C . PASS AS_SB_TABLE=0,169|0,36;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=207;AS_FilterStatus=SITE;MBQ=38,38;MFRL=238,236;MMQ=60,60;MPOS=22;POPAF=1.18;TLOD=107.23 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:169,36:0.179:205:89,20:78,16:0,169,0,36
chr8 128742851 . C T . PASS AS_SB_TABLE=244,378|21,33;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=692;AS_FilterStatus=SITE;MBQ=38,38;MFRL=165,173;MMQ=60,60;MPOS=16;POPAF=0.609;TLOD=137.47 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:622,54:0.084:676:316,24:234,25:244,378,21,33
chr8 128742960 . C T . PASS AS_SB_TABLE=16,209|1,22;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=263;AS_FilterStatus=SITE;MBQ=38,38;MFRL=212,211;MMQ=60,60;MPOS=25;POPAF=2.23;TLOD=60.6 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:225,23:0.095:248:131,13:86,6:16,209,1,22
chr8 128748307 MantaDUP:TANDEM:368:0:1:0:0:0 C <DUP:TANDEM> . . END=128749008;SVTYPE=DUP;SVLEN=701;CIPOS=0,5;CIEND=0,5;HOMLEN=5;HOMSEQ=GGCTG;UPSTREAM_PAIR_COUNT=1;DOWNSTREAM_PAIR_COUNT=1;PAIR_COUNT=1 . .
chr8 128750540 . A G . PASS AS_SB_TABLE=693,617|226,191;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=1824;AS_FilterStatus=SITE;MBQ=38,38;MFRL=164,171;MMQ=60,60;MPOS=17;POPAF=1.6;TLOD=1242.89 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:1310,417:0.249:1727:597,183:522,177:693,617,226,191
chr8 128751201 . G A . PASS AS_SB_TABLE=285,654|31,96;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=1152;AS_FilterStatus=SITE;MBQ=38,38;MFRL=170,179;MMQ=60,60;MPOS=19;POPAF=1.35;TLOD=343.68 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:939,127:0.122:1066:419,50:436,66:285,654,31,96
chr8 128752846 . C T . PASS AS_SB_TABLE=1251,876|88,68;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=2376;AS_FilterStatus=SITE;MBQ=38,38;MFRL=180,185;MMQ=60,60;MPOS=18;POPAF=7.3;TLOD=374.98 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:2127,156:0.067:2283:1114,79:814,58:1251,876,88,68
chr8 128758861 . T C . germline AS_SB_TABLE=133,156|145,172;ECNT=1;GERMQ=1;SOURCES=mutect2;DP=635;AS_FilterStatus=SITE;MBQ=38,38;MFRL=165,165;MMQ=60,60;MPOS=20;POPAF=0.323;TLOD=1085.95 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:289,317:0.521:606:154,160:112,129:133,156,145,172
chr8 128767593 . C T 0 LowFisherScore;LowVafTumor;LowAltCntTumor;StrandBias SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=25;SB=0;SOURCES=lancet GT:AD:SR:SA:DP 0/1:53,2:53,0:2,0:55
chr8 128767687 . G C 0 LowFisherScore SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=25;SB=6.79507;SOURCES=mutect2,lancet GT:AD:SR:SA:DP 0/1:163,12:93,70:6,6:175
chr8 128767857 . A G 0 LowFisherScore;StrandBias SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=25;SB=0;SOURCES=lancet GT:AD:SR:SA:DP 0/1:65,4:0,65:0,4:69
chr8 128767876 . T C 0 LowFisherScore;StrandBias SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=25;SB=0;SOURCES=lancet GT:AD:SR:SA:DP 0/1:38,4:0,38:0,4:42
chr8 128773207 . G C . PASS AS_SB_TABLE=47,70|83,181;ECNT=1;GERMQ=74;SOURCES=mutect2;DP=395;AS_FilterStatus=SITE;MBQ=38,38;MFRL=161,166;MMQ=60,60;MPOS=14;POPAF=0.25;TLOD=921.97 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:117,264:0.693:381:60,143:42,92:47,70,83,181
chr8 128779001 . G A . PASS AS_SB_TABLE=289,202|86,46;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=638;AS_FilterStatus=SITE;MBQ=38,38;MFRL=182,192;MMQ=60,60;MPOS=15;POPAF=0.471;TLOD=387.04 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:491,132:0.214:623:281,74:165,48:289,202,86,46
chr8 128788985 . A G . germline AS_SB_TABLE=282,264|336,273;ECNT=1;GERMQ=1;SOURCES=mutect2;DP=1229;AS_FilterStatus=SITE;MBQ=38,38;MFRL=167,172;MMQ=60,60;MPOS=19;POPAF=0.145;TLOD=2051.61 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:546,609:0.526:1155:265,332:228,215:282,264,336,273
chr8 128789075 . G T . PASS AS_SB_TABLE=234,611|21,80;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=1008;AS_FilterStatus=SITE;MBQ=38,38;MFRL=173,186;MMQ=60,60;MPOS=18;POPAF=2.63;TLOD=260.28 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:845,101:0.107:946:468,47:285,44:234,611,21,80
chr8 128802021 . A C . PASS AS_SB_TABLE=319,309|127,164;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=956;AS_FilterStatus=SITE;MBQ=38,38;MFRL=167,166;MMQ=60,60;MPOS=16;POPAF=0.415;TLOD=904.53 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:628,291:0.32:919:329,164:225,95:319,309,127,164
chr8 128808785 . T C 0 LowFisherScore;LowVafTumor;LowAltCntTumor;StrandBias SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=21;SB=0.627699;SOURCES=lancet GT:AD:SR:SA:DP 0/1:228,2:212,16:2,0:230
chr8 128808839 . T C 0 LowFisherScore SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=21;SB=13.6758;SOURCES=mutect2,lancet GT:AD:SR:SA:DP 0/1:197,299:124,73:174,125:496
chr8 128815029 . T C . germline AS_SB_TABLE=102,251|130,333;ECNT=1;GERMQ=1;SOURCES=mutect2;DP=825;AS_FilterStatus=SITE;MBQ=38,38;MFRL=177,174;MMQ=60,60;MPOS=18;POPAF=0.13;TLOD=1592.7 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:353,463:0.562:816:202,247:120,162:102,251,130,333
chr8 128822709 . A G . germline AS_SB_TABLE=126,155|113,113;ECNT=1;GERMQ=1;SOURCES=mutect2;DP=535;AS_FilterStatus=SITE;MBQ=38,38;MFRL=173,177;MMQ=60,60;MPOS=19;POPAF=0.367;TLOD=754.65 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:281,226:0.442:507:132,104:97,76:126,155,113,113
chr8 128829558 . G C 3.88324 LowFisherScore;HighVafNormal;HighAltCntNormal SHARED;FETS=3.88324;TYPE=snv;LEN=1;KMERSIZE=21;SB=18.4493;SOURCES=mutect2,lancet GT:AD:SR:SA:DP 0/1:198,136:11,187:1,135:334
chr8 128838615 . T C . PASS AS_SB_TABLE=246,202|147,124;ECNT=1;GERMQ=40;SOURCES=mutect2;DP=777;AS_FilterStatus=SITE;MBQ=38,38;MFRL=167,169;MMQ=60,60;MPOS=18;POPAF=0.25;TLOD=864.44 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:448,271:0.375:719:227,120:176,119:246,202,147,124
chr8 128844586 . C T . PASS AS_SB_TABLE=335,34|59,6;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=449;AS_FilterStatus=SITE;MBQ=38,38;MFRL=182,185;MMQ=60,60;MPOS=15;POPAF=1.52;TLOD=181.95 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:369,65:0.152:434:186,35:160,25:335,34,59,6
chr8 128844721 . G A . germline AS_SB_TABLE=47,124|47,174;ECNT=1;GERMQ=1;SOURCES=mutect2;DP=397;AS_FilterStatus=SITE;MBQ=38,38;MFRL=180,186;MMQ=60,60;MPOS=19;POPAF=0.223;TLOD=804.44 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:171,221:0.569:392:94,134:63,79:47,124,47,174
chr8 128852202 . G A . PASS AS_SB_TABLE=94,63|49,31;ECNT=1;GERMQ=10;SOURCES=mutect2;DP=249;AS_FilterStatus=SITE;MBQ=38,38;MFRL=153,152;MMQ=60,60;MPOS=20;POPAF=0.349;TLOD=246.38 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:157,80:0.327:237:87,43:59,27:94,63,49,31
chr8 128858597 . C G . PASS AS_SB_TABLE=514,101|63,4;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=698;AS_FilterStatus=SITE;MBQ=38,38;MFRL=191,201;MMQ=60,60;MPOS=17;POPAF=1.44;TLOD=186.77 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:615,67:0.104:682:317,33:262,34:514,101,63,4
chr8 128858689 . G A . PASS AS_SB_TABLE=374,282|174,162;ECNT=2;GERMQ=93;SOURCES=mutect2;DP=1057;AS_FilterStatus=SITE;MBQ=38,38;MFRL=166,169;MMQ=60,60;MPOS=19;POPAF=0.272;TLOD=1083.39 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:656,336:0.343:992:327,185:262,120:374,282,174,162
chr8 128858733 . G A . PASS AS_SB_TABLE=345,502|60,94;ECNT=2;GERMQ=93;SOURCES=mutect2;DP=1021;AS_FilterStatus=SITE;MBQ=38,38;MFRL=160,159;MMQ=60,60;MPOS=23;POPAF=7.3;TLOD=440.54 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:847,154:0.157:1001:356,72:249,44:345,502,60,94
chr8 128864331 . A G . germline AS_SB_TABLE=144,150|170,128;ECNT=1;GERMQ=1;SOURCES=mutect2;DP=616;AS_FilterStatus=SITE;MBQ=38,38;MFRL=169,175;MMQ=60,60;MPOS=16;POPAF=0.197;TLOD=1023.27 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:294,298:0.503:592:153,160:117,120:144,150,170,128
chr8 128879751 . G A . PASS AS_SB_TABLE=246,117|30,11;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=411;AS_FilterStatus=SITE;MBQ=38,38;MFRL=169,181;MMQ=60,60;MPOS=21;POPAF=0.728;TLOD=101.48 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:363,41:0.101:404:193,14:125,22:246,117,30,11
chr8 128879839 . G A . PASS AS_SB_TABLE=137,210|43,54;ECNT=1;GERMQ=93;SOURCES=mutect2;DP=458;AS_FilterStatus=SITE;MBQ=38,38;MFRL=165,161;MMQ=60,60;MPOS=17;POPAF=0.432;TLOD=279.71 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:347,97:0.217:444:176,40:115,40:137,210,43,54
chr8 128889092 . C G 0 LowFisherScore;StrandBias SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=13;SB=0;SOURCES=lancet GT:AD:SR:SA:DP 0/1:29,12:29,0:12,0:41
chr8 128889285 . C A 0 LowFisherScore SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=13;SB=13.7992;SOURCES=mutect2,lancet GT:AD:SR:SA:DP 0/1:147,360:120,27:275,85:507
chr8 128889348 . A T 0 LowFisherScore;LowVafTumor SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=13;SB=4.25971;SOURCES=lancet GT:AD:SR:SA:DP 0/1:748,3:373,375:2,1:751
chr8 128889363 . C T 0 LowFisherScore;LowVafTumor;LowAltCntTumor;StrandBias SOMATIC;FETS=0;TYPE=snv;LEN=1;KMERSIZE=17;SB=8.80762;SOURCES=lancet GT:AD:SR:SA:DP 0/1:259,2:93,166:2,0:261
chr8 128889370 . GAC GCG 0 LowFisherScore SOMATIC;FETS=0;TYPE=complex;LEN=2;KMERSIZE=13;SB=13.6052;SOURCES=lancet GT:AD:SR:SA:DP 0/1:303,273:126,177:103,170:576