[BioC] base-specific read counts

[Yu Chuan Tai]

Hi Sean,

I didn't find any function in  the VariantAnnotation package that can 
calculate mutant freq. Do you mean after reading in a VCF file using 
readVcf(), I need to calculate the base-level coverage first (for example, 
using the way Martin had suggested), and convert coverage to frequency 
myself? Then why do I need to use VariantAnnotation package for this 
purpose, given the fact that I already have a text file with all the 
SNVs/INDELs with their genomic coordinates?

Best,
Yu Chuan

On Fri, 8 Jun 2012, Sean Davis wrote:

> 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
>