If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.We appreciate your help!
Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
How read groups affect Variant Calling?
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?
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