[BioC] base-specific read counts

[Yu Chuan Tai]

Hi Sean,

No worries. I actually want mutant frequencies for each sample, but I 
didn't see any fucntion in VariantAnnotation for that. Anyway, I just 
found that samtools/bcftools may calculate that directly.

Thanks for your help!
Best,
Yu Chuan

On Sat, 9 Jun 2012, Sean Davis wrote:

> 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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>