extract duplicated reads

ShouyongPengShouyongPeng BostonPosts: 1Member

Hi

It would be great if we can extract duplicated reads and check where they fall on the genome.

Shouyong

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Answers

  • pdexheimerpdexheimer Posts: 483Member, GATK Dev, DSDE Dev mod

    Since they're flagged in the BAM file, this isn't too hard. I use samtools for tasks like this: samtools view -f 0x400 -b -o Sample_dupes.bam Sample.bam

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 8,163Administrator, GATK Dev admin

    Ah, that's a good idea. Much simpler than writing a new read filter :)

    Geraldine Van der Auwera, PhD

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