local realignment without known indels

gilgigilgi Posts: 19Member
edited July 2012 in Ask the GATK team

Dear GATK team,

I understood from the best practice documentation that if I have no known indels list for the genome I can skip the realignment step. Is this correct, or shall I call Indels and then do realignment and then re-call SNPs and Indels with the UnifiedGenotyper?

Thanks for the help!

Best Answer

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 6,822Administrator, GATK Developer admin
    Answer ✓

    Hi there,

    You can run those tools on a merged bam file, or by passing several separate bam files in your command line (see the documentation if you're not sure how to do this).

    There are no hard and fast numbers for file sizes -- it depends enormously on your dataset and on your computing hardware. I can only recommend you test a few different configurations and see what works for you.

    Geraldine Van der Auwera, PhD

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