To celebrate the release of GATK 4.0, we are giving away free credits for running the GATK4 Best Practices pipelines in FireCloud, our secure online analysis portal. It’s first come first serve, so sign up now to claim your free credits worth $250. Sponsored by Google Cloud. Learn more at https://software.broadinstitute.org/firecloud/documentation/freecredits

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?

Thank you,

Best Answer

Answers

Sign In or Register to comment.