need to run a step with FixMateInformation after realignment step ?

TiphaineTiphaine Posts: 53Member
edited January 2013 in Ask the GATK team

Dear Community and GATK's team,

I have one question about the cleaning step before SNP calling, mainly about local realignment around indels.

I read on some website describing their workflow that alignments may change during the realignment process, it would prefer to fix the mate information and Picard offers this utility to do that for us. is it true? Or are there only any insert sizes that can change? If there are some change of insert sizes, is there a tool that checks that these changes are ok?

What do you use Picard's tool, FixMateInformation.jar, to fix the mate information when using paired-end data ?

Up to now, I have not used in my pipeline. Maybe this is a mistake. If we have to add this step, should we add this step after the realignment step or recalibration step?

Thank you for your help,


Post edited by Geraldine_VdAuwera on

Best Answer

  • Mark_DePristoMark_DePristo Posts: 153Administrator, GATK Developer admin
    Answer ✓

    The indel realigner fixes mates itself, so the file is valid after realignment. How this is accomplished is a bit of magic code from Eric Banks and myself from several years ago. A previous version of the realigner did require you to run two passes, but that was before the magic code was written.

    -- Mark A. DePristo, Ph.D. Co-Director, Medical and Population Genetics Broad Institute of MIT and Harvard


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