[BioC] base-specific read counts

[Yu Chuan Tai]

Hi Martin,

One more question. Is there any way in Rsamtools to calculate SNVs/INDELS 
frequency directly using the output file from samtools?
Thanks!

Best,
Yu Chuan

On Thu, 7 Jun 2012, Martin Morgan wrote:

> On 06/06/2012 10:43 PM, Yu Chuan Tai wrote:
>> Hi,
>> 
>> Is there any way to calculate base-specific read counts for a given
>> genomic interval (including 1-base interval), for paired-end data
>> aligned by Bowtie2 in BAM format?
>
> Thanks for posting to the Boic mailing list! Functions like 
> readGappedAlignments, scanBam, etc. take an argument ScanBamParam that in 
> turn has an argument 'which' to specify, using GRanges, the regions of a bam 
> file you want to query
>
>  gwhich <- GRanges("chr1", IRanges(c(1000, 2000, 3000), width=100)),
>      c("+", "+", "-"))
>  param <- ScanBamParam(which=gwhich)
>  scanBam("my.bam", param=param)
>
> Base-level coverage is also available with ?applyPileups, see 
> example(applyPileups).
>
> Martin
>
>> Thanks!
>> 
>> Best,
>> Yu Chuan
>> 
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