[BioC] base-specific read counts

[Sean Davis]

On Fri, Jun 8, 2012 at 2:06 AM, Yu Chuan Tai <yuchuan at stat.berkeley.edu> wrote:
> Hi Martin,
>
> One more question. Is there any way in Rsamtools to calculate SNVs/INDELS
> frequency directly using the output file from samtools?

By "output file from samtools", I assume you mean a VCF file.  If so,
take a look a the VariantAnnotation package and readVcf().  From
there, you'll need to do the calculation yourself, but that would be a
step on the way to accomplishing your task.

Sean