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

How to use --setFilteredGtToNocall and --maxNOCALLfraction with SelectVariants

timflutretimflutre Montpellier, FranceMember
edited June 2017 in Ask the GATK team


I have a VCF file on which I first use VariantFiltration (GATK v3.7) with various filter expressions, such as "QD < 2.0" and "MQ < 40.0", as well as various genotype filter expressions, such as "DP < 10" and "GQ < 20".

I then use SelectVariants with --excludeFiltered and --excludeNonVariants, but also with --setFilteredGtToNocall, --maxFractionFilteredGenotypes 0.300000 and --maxNOCALLfraction 0.300000.

However, in the end, the output VCF file still contains a site with more than 30% missing genotypes.

To discard such a site, I have to run SelectVariants twice, the second time only with --maxNOCALLfraction 0.300000.

It hence looks like --setFilteredGtToNocall and --maxNOCALLfraction have to be used sequentially, in two different runs of SelectVariants. Am I right?

Best regards,

Issue · Github
by Sheila

Issue Number
Last Updated


Sign In or Register to comment.