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number of variants and mutations

BogdanBogdan Palo Alto, CAMember ✭✭

Dear all,

if I may ask a very simple question and very general : for a normal WGS sample (at least 30X), on average, how many variants would HaplotypeCaller typically produce in the VCF file ? And for a normal-tumor pairs (coverage at least 50x), how many mutations would Mutect1 or Mutect2 report ? many thanks,



  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    To be honest we don't like to give expected numbers because they are so easily subject to misinterpretation and vary a lot depending on the quality of your data and how you're running the tools. If we did we'd get loads of questions from people who aren't getting exactly the same numbers, all asking if their particular number is normal. Then it never ends.

    We'd rather people look at the literature to find out what is the estimated number of variants in a typical individual of the organism they're studying (not everyone works on humans, which I assume is what you're asking about). Then our answer is: our tools will call most if not all of those, plus a bunch more where "a bunch" varies wildly depending on the quality of your data and the stringency of the filters you apply.

  • BogdanBogdan Palo Alto, CAMember ✭✭

    thank you Geraldine, happy weekend !

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