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RealignerTargetCreator with reduced representation libraries

cookethocooketho Member
edited August 2012 in Ask the GATK team

My bam files contain reads from a reduced representation library where the genomic DNA was digested with restriction enzymes--so every paired-end read starts with a restriction site. Will this affect how GATK discovers regions that require realignment, or the effectiveness of the realignment itself?

Best Answer

  • Mark_DePristoMark_DePristo Broad Institute admin
    Accepted Answer

    We've never run the GATK on such an input BAM. It may work well, but also may not. You'll have to explore this yourself, as we don't have any specific advice to give you. It's likely that you will need to revise your calling pipeline a bit to make this work effectively.

Answers

  • Mark_DePristoMark_DePristo Broad InstituteMember admin
    Accepted Answer

    We've never run the GATK on such an input BAM. It may work well, but also may not. You'll have to explore this yourself, as we don't have any specific advice to give you. It's likely that you will need to revise your calling pipeline a bit to make this work effectively.

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