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?