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How do I find input arguments (RGPU, RGLB, etc) for AddOrReplaceReadGroups

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
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updated by Devon Ryan Devon Ryan • written by Max Max

1 answer

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

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written by Devon Ryan Devon Ryan

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

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written by Max Max

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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written by Devon Ryan Devon Ryan

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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written by Max Max

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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written by Andrés Ribone • Andrés Ribone

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