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Setting BOTH or POOLBOTH for HaplotypeCaller for multiple individuals of a population?

skblazerskblazer Member
edited August 2012 in Ask the GATK team

Hi,

I'd like to feed HaplotypeCaller with several BAM files for different individuals of a population simultaneously, but I need to genotype alleles for each individuals. Which option do I need set -glm with, BOTH or POOLBOTH?

Another question, I've known GATK won't consider BAQ for calling indels, but when I set -glm with BOTH, if GATK will also turn off BAQ for SNP calling?

Thanks,
SK

Best Answer

  • ebanksebanks Broad Institute ✭✭✭✭
    Accepted Answer

    The -glm option is not relevant with the HaplotypeCaller (it is ignored). We will soon be separating out those arguments that are common to both the HaplotypeCaller and UnifiedGenotyper and those which relate only to the UG (like this one).

    BAQ is only used for calling SNPs if enabled, but when it is enabled using -glm both will not turn it off for SNPs.

Answers

  • ebanksebanks Broad InstituteMember, Broadie, Dev ✭✭✭✭
    Accepted Answer

    The -glm option is not relevant with the HaplotypeCaller (it is ignored). We will soon be separating out those arguments that are common to both the HaplotypeCaller and UnifiedGenotyper and those which relate only to the UG (like this one).

    BAQ is only used for calling SNPs if enabled, but when it is enabled using -glm both will not turn it off for SNPs.

  • skblazerskblazer Member

    Thanks. So you means I don't need set -glm, and HaplotypCaller will defaultly call both SNPs and Indels?

  • ebanksebanks Broad InstituteMember, Broadie, Dev ✭✭✭✭
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