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.
Haplotype caller BP_RESOLUTION :More AD values than alleles called for
My intention is to find different bases called in a particular chromosome location irrespective of it being assigned as SNP/badbase. I user the below command:
java -jar 3.5/GenomeAnalysisTK.jar -T HaplotypeCaller -R Reference.fa -I Sample1.bam -o Sample1.BPR.vcf -ERC BP_RESOLUTION -L 1
I got my intended result but is confused with the result for example:
1 1222274 . A . . . GT:AD:DP:GQ:PL 0/0:92,1:93:99:0,120,1800
1 8333303 . A AG,AT,G,T, 0 . BaseQRankSum=0.913;ClippingRankSum=-0.141;DP=57;ExcessHet=3.0103;MLEAC=0,0,0,0,0;MLEAF=0.00,0.00,0.00,0.00,0.00;MQRankSum=0.445;RAW_MQ=205200.00;ReadPosRankSum=-0.85GT:AD:DP:GQ:PL:SB 0/0:39,2,5,2,2,0:50:36:0,79,1151,36,1041,1086,88,985,919,1611,88,985,919,1546,1611,110,942,900,957,957,928:10,29,3,8
Why there are more values for AD than the number of Alleles called for. Please note I am working with RNAseq dataset after BQSR