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

Filteration creteria

i want to filter a vcf file resulted GATK. my criterias are QUAL < 30, FS > 60, MQ < 30, DP < 10 and GQ < 30.
filterExpression in my command line in GATK must be as following? GQ is in right place in command? another question is QD < 2 is good criteria for quality filteration?

--filterExpression "QUAL < 30 || FS > 60.0 || MQ < 30.0 || DP < 10 || GQ < 30"

thanks in advance

Best Answer

Answers

Sign In or Register to comment.