[BioC] alignment & SNP calling

[Kasper Daniel Hansen]

On Tue, Nov 16, 2010 at 3:34 AM, Andreia Fonseca
<andreia.fonseca at gmail.com> wrote:
> quality scores. Other aligners like Bowtie are possible but don't use
> quality scores. Then in Bioconductor there are packages to take in the
> output and make some statistcs from it.

This is not true.   Bowtie implements the MAQ model for dealing with
qualities.  Whether it makes sense to use that model is another issue,
but the capability is there.  And it is much faster.

Kasper