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Large cohort VCFs in GATK4 - to combine or not ...
I've somatically called a few thousand samples against a PoN. I'm now looking through the results and wondering how best to collate all these single VCFs. Is there a tool like GenotypeGVCF for VCFs? (CombineVariants is no longer available - and would take too long presumably).
If not, what would be a strategy for pooling these result files into an analysis set? Is there an alternative analysis strategy to pooling?