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multiple alleles in a diploid genome

Dear Team

When running UnifiedGenotyper (GATK 2.3-9), I checked the running log, and kept seeing the warning message: "DiploidExactAFCalc - this tool is currently set to genotype at most 3 alternate alleles in a given context...."
I set max alternate alleles to be 3 here. However, I remember that this information was minimal (or even none) when I run GATK 1.6.5 on the same dataset. Do I need to take any caution on these warning messages? You can see the attached figure that this information is a lot during a complete run... just a bit worry if the real alternate alleles will be picked up if the program sees multiple alleles on the same locus.



  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    You don't need to worry about it. This limitation was added to improve performance (the more alternate alleles you consider, the greater the computational cost) and should be safe for a diploid organism. The program will keep the most likely alleles and discard the least likely alternates. If you do still worry, you can always look up a few of those positions in IGV, compare the pileup to the resulting calls, and see if there are any calls that look like real alternates were omitted.

  • Hey,

    if you worry to miss something leave the "--max_alternate_alleles" argument unchanged (Default value is 6) or set it up instead of down (may be more computational demanding).
    Anyway i don't think you will miss a lot as most of these will be problematic sites with InDels...

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