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Parallelizing VariantFiltration

GATK Team,

Currently in our variant calling pipeline, one step is to use VariantFiltration to flag any genotype calls with low confidence (defined to be GQ<20). I noticed that the VariantFiltration tool is not parallelizable (either -nt or -nct), while the ApplyRecalibration tool is (via -nt). From a novice, it seems that the same logic to parallelize ApplyRecalibration could be used to parallelize VariantFiltration. Is this the case, or is there something deeper that is different between the two? If VariantFiltration is paralleizable, is this currently in the works? Can I request this feature (and help)?

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by Sheila

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