Remove duplicate reads from the DepthOfCoverage

gtg269cgtg269c Posts: 1Member
edited January 2013 in Ask the GATK team

I was wondering if there is an option to remove duplicate reads when the coverage is determined using DepthOfCoverage from a .BAM file. Or is there an alternate way to remove the duplicate reads.


Post edited by Geraldine_VdAuwera on


  • ebanksebanks Broad InstitutePosts: 690Member, Administrator, GATK Dev, Broadie, Moderator, DSDE Dev, GP admin

    Hi Amin,

    Reads that are marked in the bam as duplicates are removed by the Depth Of Coverage tool automatically - there's nothing you need to do, assuming you have used a tool to mark the duplicates first (see our best practices for more details).

    Eric Banks, PhD -- Director, Data Sciences and Data Engineering, Broad Institute of Harvard and MIT

  • adamchieefadamchieef Posts: 1Member

    Remove all duplicates by using Duplicate Files Deleter

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 8,737Administrator, GATK Dev admin

    That has got nothing to do with the question, @adamchieef.

    Geraldine Van der Auwera, PhD

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