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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

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