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.
Resource Annotation by Variant rather than Site
I would like to have certain annotations applied only if the variants in the resource and the target have the same genomic change. Ex: In Cosmic the following variants are present.
12 25398284 . C G . PASS Genename=KRAS;MutationAA=p.G12A;MutationCDS=c.35G>C 12 25398284 . C A . PASS Genename=KRAS;MutationAA=p.G12V;MutationCDS=c.35G>T 12 25398284 . C T . PASS Genename=KRAS;MutationAA=p.G12D;MutationCDS=c.35G>A
However, in my VCF file I get the G12A annotation for all variants at this site even if the actual change is G12V or G12D.
Is this possible?