skip "indel realignment" and recalibration"

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

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Best Answers

  • shleeshlee Cambridge admin
    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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