-T CombineVariants question

-T CombineVariants
-genotypeMergeOptions UNIQUIFY
Is UNIQUIFY the default?
I want every variant in the output file with each individual in the same column

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Answers

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    It's a little complicated because it depends on the value of the priority order argument. If you don't specify an option, the tool will check whether you specified a priority order. If yes, merging option will be set to PRIORITIZE. If not, merging will be set to UNSORTED.

    If you want UNIQUIFY you have to specify it.

  • Nick_BeesonNick_Beeson Member

    I did not write a clear question. Sorry.
    When I use the walker -T CombineVariants, I want all of the variants from all of the files in the new file. For simplicity imagine I am combining three files each with one individual, when only one of these file has a variant, I want the resultant file to have three entries for that variant, showing the other two as calling 0/0. Does this walker do that? What options do I have to set to get it to do that?

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