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Biallelic variants only with HaplotypeCaller

I want to restrict the HaplotypeCaller to only call biallelic sites. I'm thinking that this can be accomplished with --max_alternate_alleles, although I'm not 100% whether this parameter should be set to 1 or 2 (one alternate allele, or two different alleles?).

--max_genotype_count seems relevant here also, but I don't understand what it does.

Basically, how do I ensure calling only biallelic sites?


  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie

    Those parameters are mainly intended to limit complexity and improve performance in messy regions, so I can't guarantee that will work well for your use case. But it's worth trying. However I would recommend using --max_genotype_count which may be a more principled way of looking for biallelic sites. The idea is that the program will look at the possible genotypes given the observed alleles, and eliminate alleles based on the amount of support they have in reads until it reaches the requested threshold for number of genotypes.

  • Thanks @Geraldine_VdAuwera

    Ok, if I do this, I will use --max_genotype_count=2.

    I understand that this functionality speeds up the variant calling process. It seems to me that most software doesn't even consider multiallelic sites, so calling them seems like a waste of time. This is basically why I wanted to try this.

  • SheilaSheila Broad InstituteMember, Broadie, Moderator


    That is fine, but if you are looking for only biallelic sites, you should set --max_genotype_count 3. There will be 3 possible genotypes with two alleles.


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