PrintReads for Pair-ended Reads

maramara Posts: 10Member

Extracting reads from a BAM file using PrintReads will give only the reads at a given loci (and not its pair). Is there a way to extract reads covering a certain locus in addition to its matched pair?

Thank you!

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Answers

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 8,171Administrator, GATK Dev admin

    Interesting idea -- unfortunately we currently don't have that capability, but we'd be interested in looking at a patch if someone wanted to implement it.

    Geraldine Van der Auwera, PhD

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