How read groups affect Variant Calling?
Posted in Ask the GATK team | Last updated on 2013-01-14 14:32:46


Comments (12)

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


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