We've moved!
This site is now read-only. You can find our new documentation site and support forum for posting questions here.
Be sure to read our welcome blog!

skip "indel realignment" and recalibration"

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

Tagged:

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.

Answers

Sign In or Register to comment.