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How to use HaplotypeCaller for paired samples?

I have paired disease-normal data sets for each sample. If I want to call SNPs and in-dels using HaplotypeCaller, how should I proceed?


  • SkyWarriorSkyWarrior TurkeyMember ✭✭✭

    Is this about somatic variants like cancer samples?

    If you are looking to find low frequency variants in somatic samples you need to look at MuTect. HC is only for germline variants.

  • Esita_1987Esita_1987 IndiaMember

    I have exome sequencing data for both normal and disease samples from the same patient.

    I have already used Mutect2 for somatic mutation calling. I am trying to run HaplotypeCaller for calling germline variants.

    Should I call for SNPs separately from both of them and then compare? Otherwise what should be the strategy?

  • SkyWarriorSkyWarrior TurkeyMember ✭✭✭

    Normally Mutect2 does that together. Can you check the best practices workflows for Mutect2?

  • Esita_1987Esita_1987 IndiaMember

    I just checked the best practices workflow. Thanks a lot for your help. Can you please suggest which filter should I use for germline variants? Will it be the germline_risk?

  • SheilaSheila Broad InstituteMember, Broadie ✭✭✭✭✭


    Let's back up here. Why are you running HaplotypeCaller? Do you only want to find variants in the normal samples? In that case, you will run HaplotypeCaller on the normal samples only, not on the cancer samples.


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