Readgroup assigment in bwa, bwa-mem, and bowtie2 and possible other tools does not set SM tag

[nekrut]

Setting read groups (when “automatically assign ID” is selected) does not assign SM tag, which is a requirement. This causes downstream issues with Picard etc.

[nsoranzo]

Which value should it have? The same of ID?

[jmchilton]

You can switch to full assignment and pick the collection identifier for individual fields.

[nekrut]

The same as ID would work fine but @jmchilton 's solution is better