Questions about IndelRealigner - Gap Open Penalty & Consensus

Dear GATK team,

I have two questions about IndelRealigner.

  1. Can I adjust Gap open penalty for IndelRealigner?

  2. As I understand, IndelRealigner make consensus alignments across the pre-existing alignments and aligns the reads to the consensus alignments.
    When making the consensus alignment, is it right that IndelRealigner do multiple-alignment among the pre-existing alignments(or aligned reads)? Or does it picks some of the pre-existing alignments as consensus?

I could not find any document about how exactly the IndelRealigner does its job.
If there is any useful document, could you let me know?

Thank you very much!


  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Hi there,

    1. No, there is no direct way to adjust the low-level realignment settings.

    2. Have a look at the Indel Realignment tab on the Best Practices documentation page; it groups all the relevant docs. Be sure to watch the workshop videos as they give additional details that you may find useful.

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