[Bioc-sig-seq] Getting optional fields from BAM file using Rsamtools
Steve Lianoglou
mailinglist.honeypot at gmail.com
Tue Mar 2 19:57:15 CET 2010
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
More information about the Bioc-sig-sequencing
mailing list