If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We appreciate your help!
Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
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?