Test-drive the GATK tools and Best Practices pipelines on Terra

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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?

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