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I am using Picard to mark only optical duplicates for which I read the manual of MarkDuplicates. My script looks like this

#!/usr/bin/bash
java -jar build/libs/picard.jar MarkDuplicates \
      I=sorted.bam \
      O=mark_opticalduplicate.bam \
      MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 \
      TAGGING_POLICY=OpticalOnly \
      M=markedoptical_dup_metrics.txt

I am not sure I am getting only optical duplicates when I am using the samtool flag 0x400 Any suggestions at this point is highly appreciated.

Bandana
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  • My interpretation of the docs is that all dupes will have flag 0x0400 and that you need to check the optional `DT` field tag to distinguish the optical dupes. https://gatk.broadinstitute.org/hc/en-us/articles/360037052812-MarkDuplicates-Picard- – Tom Morris Feb 21 '21 at 21:46
  • How can I check for the DT field? – Bandana Feb 22 '21 at 15:40

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