How do I turn off INDEL calling in HaplotypeCaller (i.e. only call SNPs)?

ktretinaktretina Baltimore, MDMember

I know that for UnifiedGenotyper the option is -glm, but I don't see that available for HaplotypeCaller.

Answers

  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin

    @ktretina

    Hi,

    You cannot disable indel calling in HaplotypeCaller. It is best to run HaplotypeCaller and get all possible variants, then remove the types you are not interested in with SelectVariants.

    -Sheila

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