Does HaplotypeCaller allow multiple allele calls?

jreevejreeve Member
edited July 2018 in Ask the GATK team

I'm trying to use HaplotypeCaller to call variants from a pooled population sample. However whenever I run the basic program, with the ploidy set to 2 x number of individuals in the pool, I get this warning;

WARN HaplotypeCallerGenotypingEngine - Removed alt alleles where ploidy is 88 and original allele count is 3, whereas after trimming the allele count becomes 2. Alleles kept are:[T*, A]

What is going on behind the scenes to reduce the allele count down to two? Is there a way to turn this off?

Cheers,
James

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  • jreevejreeve Member

    Thanks Sheila,

    I set --max-genotype-count 4096 and the message has changed to;
    WARN HaplotypeCallerGenotypingEngine - Removed alt alleles where ploidy is 88 and original allele count is 5, whereas after trimming the allele count becomes 3. Alleles kept are:[G*, A, GA]
    This suits my purposes since I'm identify multi-allelic sites to filter them out of my final dataset.

    I noticed that now HaplotypeCaller is running much slower. Is this because HaplotypeCaller is now calculating each call over a larger vector of possible genotypes?

    Also is the notation for --max-genotype-count the G value from the page you linked me?

    -James

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