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Max Alt Alleles behavior

I'm using HaplotypeCaller to call a vcf file with 8 samples. I left the --max_Alt_Alleles argument at its default 6. However I'm getting some odd warning messages:

WARN 19:12:58,670 ExactAFCalc - this tool is currently set to genotype at most 6 alternate alleles in a given context, but the context at chr1:2274306 has 26 alternate alleles so only the top alleles will be used; see the --max_alternate_alleles argument

Since I'm calling 8 samples, shouldn't the maximum number of alternate alleles be 15 (2n-1)? Or is the number of alternate alleles observed in the given context referring to the number of possible haplotypes that could possibly be constructed from the aligned reads?

Best Answer


  • ktretinaktretina Baltimore, MDMember

    As a follow-up to the question above, could you please explain how maxAltAlleles determines the "top" alleles? I'm interested in only calling the major allele using haploid organism data, and this looks like the correct option to do so.

    Issue · Github
    by Sheila

    Issue Number
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  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    We remove alternate alleles that are the least well supported until we get to the number of genotypes/max alleles requested. The estimate of allele support is based on the ranking of the candidate haplotypes coming out of the graph building step. Note that the reference allele is always kept. Note that this approach is fairly naive and should only be used to pare down the number of combinations we're willing to consider to avoid explosive situations in messy regions, not to make an absolute determination of the correct allele (since it doesn't account for the quality of the sequence supporting each allele, just its quantity).

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