Test-drive the GATK tools and Best Practices pipelines on Terra

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skip "indel realignment" and recalibration"

Hi to all
can I skip "indel realignment" and re-calibration" steps, when I am using HaplotypeCaller ?


Best Answers

  • shleeshlee Cambridge ✭✭✭✭✭
    Accepted Answer

    Hi @30yavash,

    Yes, we recommend BQSR. It is part of the Best Practices and to use an analogy from @Geraldine_VdAuwera, it is akin to purchasing fire insurance that prevents your house from burning down.


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