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local realignment without known indels

gilgigilgi Member Posts: 19
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 Cambridge, MAMember, Administrator, Broadie Posts: 11,651 admin
    Accepted 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

Answers

  • gilgigilgi Member Posts: 19

    I understand now that I need to run the RealignerTargetCreator and then the IndelRealigner tool.
    I am working on yeast barcoded targeted genome.
    The RealignerTargetCreator and the IndelRealigner are not read group aware - right?
    Would you suggest to run them on each sample separately - or on a merged file?

    One more question regarding the work on merged bam files - what is the maximal size of merged bam you recommend to work with?

    Many thanks for all the help!

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie Posts: 11,651 admin
    Accepted 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

  • gilgigilgi Member Posts: 19
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