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port CombineVariants #17
The behavior of the GATK3 CombineVariants was very inconsistent and the arguments weren't entirely clear. I also suspect that some operations weren't possible with the arguments given. Rather than port that old broken version, I would advocate for an overhaul or rewrite.
@bhanugandham it's going to be a big project to collect requirements and expected behavior for this tool. For example, what should the MQ be for the combined VCF for two different input VCFs with different MQ values? Much of the confusion stemmed from the old ability to merge VCFs containing the same sample. In the case where we take one genotype for each sample name (e.g. the old