[BioC] any package can be used to extract SNP from bam or pileup file

[Martin Morgan]

On 11/28/2012 9:09 AM, Wang Peter wrote:
> this function can be realized by bcftools
>
> but those tools have some problems

In Rsamtools the output of bcftools can be read in to R with readPileup. The 
applyPilesups function extracts pileup information (e.g., nucleotides covering 
individual reads), but requires your own processing to call SNPs, etc. The gmapR 
package provides an interface to gmap and might be an excellent choice (others 
on the list might provide end-user experience).

Martin

>
> thank you
>


-- 
Dr. Martin Morgan, PhD
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109