[Bioc-sig-seq] Getting optional fields from BAM file using Rsamtools

[Steve Lianoglou]

Hi,

I'm referencing the info that's mentioned in section 2.2.4 of the SAM
specification:
http://samtools.sourceforge.net/SAM1.pdf

Is it possible to get the information stored in there from my BAM file
using Rsamtools? I can't find any way to do so, sorry if I'm missing
something obvious.

Bowtie (and I reckon BWA, or whatever) stores the mismatch info of the
read-to-reference (eg. MD:Z:5C5C25) from there, and I'd like to be
able to get at it

Thanks,
-steve

-- 
Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact