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I'm trying to run vcfsimplify.py to filter snps from a VCF file, but it keeps returning an error (see below). Any help with this would be much appreciated.
andrea@T3610-U:~/introgressionbrowser$ vcfmerger/vcfsimplify.py -i /home/andrea/introgressionbrowser/data/PvTFL1y_refV2_Chr01.recode.vcf -o simp_snp
VCF Heap Translation None
simplifying :: SNP [ 2, 1] True
simplifying :: Heterozygous [ 4, 2] True
simplifying :: Homozygous [ 8, 3] True
simplifying :: Indel [ 16, 4] True
simplifying :: Singleton [ 32, 5] True
Progress Legend:
print every : 1000
Heterozygous Dest : h
Homozygous : o
Heterozygous Indel: I
Homozygous Indel : i
Source Indel : s
Singleton 1 : 1
Singleton 2 : 2
Singleton 3 : 3
Ok : .
2018-09-25T12:26:21.947195
saving to simp_snp
adding file to heap
vcf file /home/andrea/introgressionbrowser/data/PvTFL1y_refV2_Chr01.recode.vcf does exists
creating vcf handler
created vcf handler
getting first register
got first register
added to heap
STARTING CHROMOSOME Chr01
heterozygous: ACTCTCTCTCTCTC,ACTCTCTCTCTCTCTC
heterozygous: C,G
heterozygous: G,T
heterozygous: A,T
heterozygous: A,G
heterozygous: C,T
heterozygous: A,T
heterozygous: A,G
heterozygous: C,T
Traceback (most recent call last):
File "vcfmerger/vcfsimplify.py", line 127, in
main(sys.argv[1:])
File "vcfmerger/vcfsimplify.py", line 105, in main
lines.append( str( val ) )
File "/home/andrea/introgressionbrowser/vcfmerger/vcfmerger.py", line 362, in str
vcfResult.simpliStats['Homozygous Indel'] += 1
KeyError: 'Homozygous Indel'
The text was updated successfully, but these errors were encountered:
I'm trying to run vcfsimplify.py to filter snps from a VCF file, but it keeps returning an error (see below). Any help with this would be much appreciated.
andrea@T3610-U:~/introgressionbrowser$ vcfmerger/vcfsimplify.py -i /home/andrea/introgressionbrowser/data/PvTFL1y_refV2_Chr01.recode.vcf -o simp_snp
VCF Heap Translation None
simplifying :: SNP [ 2, 1] True
simplifying :: Heterozygous [ 4, 2] True
simplifying :: Homozygous [ 8, 3] True
simplifying :: Indel [ 16, 4] True
simplifying :: Singleton [ 32, 5] True
Progress Legend:
print every : 1000
Heterozygous Dest : h
Homozygous : o
Heterozygous Indel: I
Homozygous Indel : i
Source Indel : s
Singleton 1 : 1
Singleton 2 : 2
Singleton 3 : 3
Ok : .
2018-09-25T12:26:21.947195
saving to simp_snp
adding file to heap
vcf file /home/andrea/introgressionbrowser/data/PvTFL1y_refV2_Chr01.recode.vcf does exists
creating vcf handler
created vcf handler
getting first register
got first register
added to heap
STARTING CHROMOSOME Chr01
heterozygous: ACTCTCTCTCTCTC,ACTCTCTCTCTCTCTC
heterozygous: C,G
heterozygous: G,T
heterozygous: A,T
heterozygous: A,G
heterozygous: C,T
heterozygous: A,T
heterozygous: A,G
heterozygous: C,T
Traceback (most recent call last):
File "vcfmerger/vcfsimplify.py", line 127, in
main(sys.argv[1:])
File "vcfmerger/vcfsimplify.py", line 105, in main
lines.append( str( val ) )
File "/home/andrea/introgressionbrowser/vcfmerger/vcfmerger.py", line 362, in str
vcfResult.simpliStats['Homozygous Indel'] += 1
KeyError: 'Homozygous Indel'
The text was updated successfully, but these errors were encountered: