If I execute "AddOrReplaceReadGroups" on a sorted and duplicate-marked .bam file, do I have to re-sort and re-mark duplicates?
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13 months ago
javiflaja ▴ 50

I'm brand new in Bioinformatics, and building my first variant calling pipeline for human genomes. Now, I got stuck using BaseRecalibrator as it needs read groups in my .bam file, so I took my sorted_dedup_output.bam and ran Picard AddOrReplaceReadGroups.

Is it necessary for me to reapply a sorting and duplicate marking step? Thanks in advance! Very helpful community!

picard AddOrReplaceReadGroups bam read-groups • 874 views
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1) read groups should have been specified from the start (eg. with bwa mem -R )

2) if you do'nt specify SORT_ORDER, the order is the same https://github.com/broadinstitute/picard/blob/master/src/main/java/picard/sam/AddOrReplaceReadGroups.java#L175 , so you don't need to re-sort.

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1) I realised I was supposed to add RGs during alingment command only after I was long done with that step. But I imgined the tool "addorreplacereagroups" could be useful after, if not, what's the use of it right? 2) how about Mark-Dup?

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