input vcf files for PhaseByTransmission

yzlyzl Posts: 6Member
edited January 2013 in Ask the GATK team

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?

Thanks

Post edited by Geraldine_VdAuwera on

Answers

  • pdexheimerpdexheimer Posts: 475Member, GATK Dev, DSDE Dev mod

    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

  • ebanksebanks Broad InstitutePosts: 687Member, Administrator, GATK Dev, Broadie, Moderator, DSDE Dev, GP Member admin

    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

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