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  • doc.ramses
    Member
    • Jan 2011
    • 26
    #1

    GATK select variants

    Hi,

    assume I have 2 .vcf files from 2 individual samples which I would like to combine with GATK CombineVariants function. Then I would like to filter in a way that I end up only with variants that are present in both samples e.g. through GATK SelectVariants function. Or is there a better way ? Can anyone tell me how to do this ?

    Thanx !
    Tags: None
    • swbarnes2
      Senior Member
      • May 2008
      • 910
      #2
      BEDTools can take vcfs as input, and output the overlap. Or the ones that don't overlap.

        Comment

        • doc.ramses
          Member
          • Jan 2011
          • 26
          #3
          Oh, of course - thanks for bringing me on track again! :=)

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