Hi,
I have a bam file with multiple read groups for same sample. Does variant calling algorithm (UnifiedGenotyper) will consider bam file as multiple-sample data or a single sample-data (irrespective of read groups) for calling varaints?
Eg.
Read Groups in BAM file:
@RG ID:41852 PL:illumina PU:41852 LB:nolib SM:41852p
@RG ID:41852.1 PL:illumina PU:41852 LB:nolib SM:41852s
@RG ID:41853 PL:illumina PU:41853 LB:nolib SM:41853s
@RG ID:41854 PL:illumina PU:41854 LB:nolib SM:41854p
@RG ID:41854.4 PL:illumina PU:41854 LB:nolib SM:41854s
@RG ID:41855 PL:illumina PU:41855 LB:nolib SM:41855p
@RG ID:41855.6 PL:illumina PU:41855 LB:nolib SM:41855s
Variants call in VCF file
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT 41852p 41852s 41853s 41854p 41854s 41855p 41855s
chrM 150 . T C 41679.01 PASS ABHom=0.999;AC=14;AF=1.00;AN=14;BaseQRankSum=1.362;DP=1255;DS;Dels=0.00;FS=0.000;HaplotypeScore=4.6324;MLEAC=14;MLEAF=1.00;MQ=40.73;MQ0=1;MQRankSum=-0.678;OND=3.149e-03;QD=33.21;ReadPosRankSum=1.479;SB=-2.052e+04 GT:AD:DP:GQ:PL 1/1:0,200:200:99:6075,544,0 1/1:0,200:200:99:6315,568,0 1/1:0,200:200:99:7094,599,0 1/1:1,197:198:99:6820,547,0 1/1:0,113:113:99:3624,322,0 1/1:0,200:200:99:7111,599,0 1/1:0,141:141:99:4640,403,0
Regards
Gaurav