It seems that this issue has come up a couple of times on the mailing listÖ 

http://sourceforge.net/p/bio-bwa/mailman/message/28365027/
and 
http://sourceforge.net/p/bio-bwa/mailman/message/32423732/

I think itís getting more relevant as people add more and more barcodes, fastq mapping is unappealing.

To solve my problem in the short term, Iím planning to explore 
http://picard.sourceforge.net/command-line-overview.shtml#MergeBamAlignment
to rescue the read group information, but Iím not sure thatís going to work and I view it as a short-term workaround at best.

I prefer not to write hundreds of fastq files, before aligning reads.


Would a patch adding support for preserving read group information be accepted?

It looks like it will be a bit of work to implementÖ at least
- update the sai format to store the optional tags or build a tag set -> read data store
- modify samse and sampe to write tags back to sam


Any guidance would be appreciated.


Brad

--
Brad Langhorst, Ph.D.
Applications and Product Development Scientist