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I know that PhaseByTransmission can accept a vcf file containing three samples of a trio as its input. I want to know if PhaseByTransmission can also accept three vcf files of a trio as its input?
Try it. It'll either work or error out immediately (I think it only takes one file, but am not certain).
You can always combine the three files with CombineVariants
FYI, it takes only one file - so use pdexheimer's suggestion.
Eric Banks, PhD -- Senior Group Leader, MPG Analysis, Broad Institute of Harvard and MIT