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.
Jexl commands; selecting multi or phased alleles
I am looking for a pathogenic variant in exome read data. To identify common inherited regions I would like to extract information from multiallelic sites or variants with phased data. Is there a way to select or filter variants based on this information with JEXL commands. I am familiar with "vc.getGenotype" , but only know how to specify HomRef, HomVar or Het. I would like to distinguish 0/1 from 0/2 or 1/1 from 1/2. Also, it would be very useful to identify if close proximity variants are on the same chromosome. I can read this data from the phased allele calls but is there a way to use Jexl to automate these calls?