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CombineVariants 'set' value separator is dash but can it be changed

I have a request for CombineVariants: can the separator between values in the "set=" keyword that is added to the INFO column be settable to something other than "-" (which I use in my sample names)? Comma would be nice. In fact, I think the VCF spec suggests it should be comma:

"INFO fields are encoded as a semicolon-separated series of short keys with optional values in the format: =[,data]."

You have the ##INFO line with Number=1, but it could be Number=., then use commas to separate each value in the INFO field.


Issue · Github
by Sheila

Issue Number
Last Updated


  • SheilaSheila Broad InstituteMember, Broadie admin


    This will not be done in GATK3, but I will see what the developers say for GATK4.


  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Hi @tedtoal, that's an interesting suggestion. We haven't yet ported CombineVariants to GATK4 (which has a completely new engine), and it's possible that we may not do a direct port, but instead reimplement some of its functionalities. The set annotation might become something you can annotate from VariantAnnotator (or equivalent). I agree that for parsing purposes it would be more convenient to use a comma-separated list instead of a single string with dashes. I'll put that in a ticket. That being said it will probably be a while before we get to this tool/port...

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