How to use --setFilteredGtToNocall and --maxNOCALLfraction with SelectVariants
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
--excludeNonVariants, but also with
--maxFractionFilteredGenotypes 0.300000 and
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
It hence looks like
--maxNOCALLfraction have to be used sequentially, in two different runs of
SelectVariants. Am I right?