Format of inputs : GRIDSS and bam

[samkjmkjmkjm]

java -jar //Applications/clove-0.17-jar-with-dependencies.jar -i sample10.vcf GRIDSS -b sample10.bam -c 43 44 -o clove.vcf

ERROR MESSAGE:
Reading input...
Exception in thread "main" java.lang.ArrayIndexOutOfBoundsException: 1
at au.edu.wehi.clove.Event.classifyAltGridssLumpy(Event.java:660)
at au.edu.wehi.clove.Event.createNewEventFromGRIDSSOutput(Event.java:584)
at au.edu.wehi.clove.Clove.main(Clove.java:635)

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I have 10 samples i have conducted GRIDSS on
this a peek at the vcf output:
##fileformat=VCFv4.2
##FILTER=<ID=ASSEMBLY_BIAS,Description="Mismatch between number of directly supporting reads and reads supporting via assembly.">
##FILTER=<ID=ASSEMBLY_ONLY,Description="Variant is supported only by assembly evidence.">
##FILTER=<ID=ASSEMBLY_TOO_FEW_READ,Description="Not enough reads contribute to this assembly as specified by 'assembly.minReads'">
etcetc
##gridssVersion=2.13.2-gridss
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT VN001_3_033 VN001_3_032 VN001_3_052 KH007_3_165 KH007_3_110 KH007_3_106 KH007_3_103 KH007_3_095 KH007_3_047 KH007_3_035
Pf3D7_01_v3 412 gridss0bb_2o T [Pf3D7_08_v3:1471647[T 65.80 LOW_QUAL;NO_ASSEMBLY ANRP=4;ANRPQ=52.70;ANSR=0;ANSRQ=0.00;AS=0;ASC=1X416N1X;ASQ=0.00;ASRP=0;ASSR=0;BA=0;BAQ=0.00;BASRP=0;BASSR=0;BMQ=33.18;BMQN=20.00;BMQX=57.00;BQ=310.24;BSC=18;BSCQ=221.88;BUM=4;BUMQ=88.36;BVF=22;CAS=0;CASQ=0.00;CIPOS=-208,209;CIRPOS=-143,144;CQ=65.80;EVENT=gridss0bb_2;IC=0;IMPRECISE;IQ=0.00;MATEID=gridss0bb_2h;MQ=36.40;MQN=21.00;MQX=50.00;RAS=0;RASQ=0.00;REF=0;REFPAIR=3;RP=5;RPQ=65.80;SB=0.5555556;SC=1X416N1X55M14D125M11D47M;SR=0;SRQ=0.00;SVTYPE=BND;VF=5 GT:AF:ANRP:ANRPQ:ANSR:ANSRQ:ASQ:ASRP:ASSR:BAQ:BASRP:BASSR:BQ:BSC:BSCQ:BUM:BUMQ:BVF:CASQ:IC:IQ:QUAL:RASQ:REF:REFPAIR:RP:RPQ:SR:SRQ:VF .:0.00:0:0.00:0:0.00:0.00:0:0:0.00:0:0:59.78:5:59.78:0:0.00:5:0.00:0:0.00:0.00:0.00:0:0:0:0.00:0:0.00:0 .:0.00:0:0.00:0:0.00:0.00:0:0:0.00:0:0:21.36:0:0.00:1:21.36:1:0.00:0:0.00:0.00:0.00:0:0:0:0.00:0:0.00:0 .:1.00:3:39.60:0:0.00:0.00:0:0:0.00:0:0:64.21:5:64.21:0:0.00:5:0.00:0:0.00:39.60:0.00:0:0:3:39.60:0:0.00:3 .:0.00:0:0.00:0:0.00:0.00:0:0:0.00:0:0:0.00:0:0.00:0:0.00:0:0.00:0:0.00:0.00:0.00:0:0:0:0.00:0:0.00:0 .:0.500:1:13.10:0:0.00:0.00:0:0:0.00:0:0:132.58:5:65.58:3:67.00:8:0.00:0:0.00:26.20:0.00:0:2:2:26.20:0:0.00:2 .:0.00:0:0.00:0:0.00:0.00:0:0:0.00:0:0:0.00:0:0.00:0:0.00:0:0.00:0:0.00:0.00:0.00:0:0:0:0.00:0:0.00:0 .:0.00:0:0.00:0:0.00:0.00:0:0:0.00:0:0:0.00:0:0.00:0:0.00:0:0.00:0:0.00:0.00:0.00:0:0:0:0.00:0:0.00:0 .:0.00:0:0.00:0:0.00:0.00:0:0:0.00:0:0:0.00:0:0.00:0:0.00:0:0.00:0:0.00:0.00:0.00:0:0:0:0.00:0:0.00:0 .:0.00:0:0.00:0:0.00:0.00:0:0:0.00:0:0:32.31:3:32.31:0:0.00:3:0.00:0:0.00:0.00:0.00:0:1:0:0.00:0:0.00:0 .:0.00:0:0.00:0:0.00:0.00:0:0:0.00:0:0:0.00:0:0.00:0:0.00:0:0.00:0:0.00:0.00:0.00:0:0:0:0.00:0:0.00:0

i have given the 1st line of output from GRIDSS 2.13.2
should i do anything to the output before feeding through clover??

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and for the bam file . I understand it should not be the GRIDSS output bam. but do you mean i have to input a bam file from all the bams of the 10 samples?
e.g samtools merge finalBamFile.bam *.bam

Thank you very much

Rgds
Samantha