[Bioc-sig-seq] Rsamtools readPileup with Mosaik alignments

[Steve Lianoglou]

Hi Jim,

This doesn't really answer/address any of your issues, and I'm sure
you already know all of this, but:

On Wed, Apr 21, 2010 at 11:34 AM, James MacDonald <jmacdon at med.umich.edu> wrote:
> Hi,
>
> I have found what I think is an infelicity with readPileup() when the
> alignment is done with software other than say BWA or Bowtie.
>
> I am aligning SOLiD data, so my choices are rather limited. In order to
> do gapped alignments, I used Mosaik to do the alignment and then
> converted to bam files and proceeded from there using samtools.

As of a few months ago bowtie can align SOLiD (colorspace) reads, and
I'm pretty sure BWA has been able to do that since the beginning of
(its) time.

Bowtie probably won't be helpful for you because it can't do gapped
alignments, but I'm pretty sure BWA can, no?

I guess, in short, I'm wondering if using BWA as your aligner would
sidestep your issues (for now)?

-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