[BioC] base-specific read counts

[Sean Davis]

On Fri, Jun 8, 2012 at 10:15 PM, Yu Chuan Tai <yuchuan at stat.berkeley.edu> wrote:
> 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?

My mistake.  I thought you meant the frequency of the variant in your
samples.  You are talking about allele counts?  If so, you'll need the
bam files, as Martin has suggested.  Sorry to mislead you.

Sean


> 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
>>
>
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