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



I have used VariantFiltration to filter the variants based on quality thresholds. Subsequently, SelectVariants to select the filter passed variants using "--excludeFiltered" flag in the command line. Could it be possible to use SelectVariants to select only the filter failed variants? I could not find it in the documentation of the tool. Is there any such option available?

Thank you


Best Answers


Sign In or Register to comment.