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.
Filtering out variants with missing data
I would like to use VariantFiltration to exclude variants that are missing genotypes for one or more sampled genomes. I see in the documentation that GT may not be filtered on (ie "GT (genotype) field is an exception") using --genotypeFilterExpression.
I could use --filterExpression "AN < $samplesize", but this requires dynamically setting the expected sample size. Is there another way?