Remove duplicate reads from the DepthOfCoverage

gtg269c

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.

Thanks Amin

ebanks

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).

adamchieef

Remove all duplicates by using Duplicate Files Deleter

Geraldine_VdAuwera

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