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HaplotypeCaller - number of haplotypes/alleles to allow

Lucy_genLucy_gen SheffieldMember

If I am analysing a single sample, can I specify a lower value for maxNumHaplotypesInPopulation and maxAltAlleles? Should these variables scale with the size of your sample population?

Best Answer


  • shleeshlee CambridgeMember, Broadie ✭✭✭✭✭

    HI again @Lucy_gen,

    The default values for maxNumHaplotypesInPopulation and maxAltAlleles apply to your single sample and I don't believe you should change them unless you have good reason to. So long as you are running HaplotypeCaller per sample, in reference confidence mode, these settings can be left alone.

    Are you running HaplotypeCaller on multiple samples at once?

  • Lucy_genLucy_gen SheffieldMember

    Hi shlee,
    No I am only running it on one sample at a time. The reason I was wondering about reducing the number of haplotypes and alt alleles was because clearly in my one sample there are only two haplotypes and max two alt alleles.

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