How do I find input arguments (RGPU, RGLB, etc) for AddOrReplaceReadGroups
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8.1 years ago
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I created a .bam file without read groups in the header, and am trying to correct this by using picard tools' AddOrReplaceReadGroups.

I've looked over the documention for AORRG,

http://broadinstitute.github.io/picard/command-line-overview.html#AddOrReplaceReadGroups

but I'm not sure where I obtain several of the input arguments to run this. Specifically, given a .bam file (and source fq files), how do I find:

RGLB (read group library), RGID (read group ID), RGPU (run barcode), etc? Of the arguments, the only one that's straightforward to me is RGPL (platform, i.e. illumina, solid, etc)

picard AddorReplaceReadGroups GATK • 4.6k views
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8.1 years ago

Aside from the barcode, those aren't things you find, they're things you come up with yourself.

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Thanks - where does one obtain the run barcode? Is it something that I can get from the .bamfile header?

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If a barcode was used, it'll often be in the fastq files, after the read names (e.g., @name 1:Y:barcode).

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I had looked at that, but the barcodes for each read aren't unique. I assumed that somewhere there is a unique barcode for the sample as well. In any case, I attempted to run addorreplaacereadgroups with RGPU=NONE, it gave an output .bam file, but it seems to be missing some identifiers in the header.

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Hey, about the differing barcodes: there must be a barcode that outnumber the rest for many magnitude orders, that is the cannon; the rest should differ only in one base.

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