Add option for sequencing centre in BAM file

[ewels]

Moved from SciLifeLab#35

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Bowtie 1

Output options:
--sam-RG <text>
Add <text> (usually of the form TAG:VAL, e.g. ID:IL7LANE2) as a field on the @RG header line. Specify --sam-RG multiple times to set multiple fields.
--sam-RG is ignored unless -S/--sam is also specified.

Bowtie2

SAM options: --rg <text>

Add <text> (usually of the form TAG:VAL, e.g. SM:Pool1) as a field on the @RG header line.

e.g.:

--rg CN:nameofourgroup

[jun-wan]

SAMTools can add the read group tag in the BAM file:
samtools addreplacerg [options] [-r <@rg line> | -R ] [-o <output.bam>] <input.bam>

[chuan-wang]

Fixed in PR #9