I have a list of SNPs and indels from 4 different software.
IndelGenotyper (broad tool)—for calling somatic indels
Bambino—for calling SNP/Indels
Somaticsniper—SNP calling
Varscan – indel/snp/LOH
Now my task is to compare SNP and indels from different software. I need some input as to how to do that. I only have output in VCF format for IndelGenotyper. The rest of the software have the following output format:
IndelGenotyper (VCF):
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT normal tumor
1 177 . A AC . . N_AC=295,310;N_DP=867;N_MM=3.1084745,4.6678634;N_MQ=18.840677,20.062836;N_NQSBQ=26.988136,22.908127;N_NQSMM=0.0111864405,0.13539149;N_SC=12,283,116,441;T_AC=234,239;T_DP=691;T_MM=3.2051282,4.7743363;T_MQ=20.816238,21.225664;T_NQSBQ=27.663815,23.273888;T_NQSMM=0.011976048,0.13911061;T_SC=9,225,85,367 GT:GQ 0/1:0 0/1:0
1 230 . AC A . . N_AC=218,227;N_DP=663;N_MM=4.03211,4.456422;N_MQ=16.825687,20.529816;N_NQSBQ=32.26916,29.760443;N_NQSMM=0.002770083,0.04280557;N_SC=18,200,73,363;T_AC=162,170;T_DP=465;T_MM=4.351852,4.745763;T_MQ=18.141975,21.064407;T_NQSBQ=32.513077,30.064604;T_NQSMM=0.0124533,0.045261122;T_SC=5,157,34,261 GT:GQ 0/1:0 0/1:0
1 247 . TA T . . N_AC=156,162;N_DP=392;N_MM=4.467949,4.3130436;N_MQ=20.666666,19.878262;N_NQSBQ=30.026958,30.963959;N_NQSMM=0.019897304,0.07715736;N_SC=31,125,65,165;T_AC=104,113;T_DP=267;T_MM=4.21153 ...