Is it sufficient to mark the duplicates per-sample?

akrishnaakrishna Posts: 3Member
edited March 18 in Ask the GATK team

Referring to broadinstitute.org/gatk/guide/article?id=3060, is removing duplicates necessary to be done twice, once per-lane and then per-sample?

Is it not enough to just mark the duplicates in the final BAM file with all the lanes merged, which should remove both optical and PCR duplicates (I am using Picard MarkDuplicates.jar)? So specifically, in the link above what is wrong with generating -

  • sample1_lane1.realn.recal.bam
  • sample1_lane2.realn.recal.bam
  • sample2_lane1.realn.recal.bam
  • sample2_lane2.realn.recal.bam

Then, merging them to get

  • sample1.merged.bam
  • sample2.merged.bam

and finally, include "de-dupping" only for the merged BAM file.

  • sample1.merged.dedup.realn.bam
  • sample2.merged.dedup.realn.bam
Post edited by akrishna on

Best Answer

Answers

  • akrishnaakrishna Posts: 3Member

    Is this perhaps because the quality score recalibration, which is a per-lane step, will be affected by duplicates if we do not perform duplication marking during per-lane pre-processing?

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