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.

missing AD after selectVariants from HaplotypeCaller joint variant calling


I called variants for a trio using HaplotypeCaller cohort pipeline. Since I need to do quality control on individual samples, I used SelectVariants to parse out variants for each individual. The process ran without crash/warning. However, I found most of variants are missing AD information in the "Sample" column (last column in VCF file), even some missing DP. However, those informations are in the original joint variant calling VCF file. Is there any way to recover this or this is the way? Could you also tell me the reason for this?




Sign In or Register to comment.