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

[Martin Morgan]

On 03/02/2010 10:57 AM, Steve Lianoglou wrote:
> 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

There is not, but it seems like a reasonable request; it won't happen
overnight. Martin

> 
> Thanks,
> -steve
> 


-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
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