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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: 454Member, GSA Collaborator ✭✭✭✭

    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: 684Member, Administrator, GATK Developer, Broadie, Moderator, DSDE Member, 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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