> The gmapR package provides an interface to gmap

Is this now true?  Last I checked it only seemed to run gsnap (not that the
latter is a bad thing, just meant for < 200bp reads).

Rsubread can also call SNPs, though it isn't as refined and polished as
gmapR.



On Wed, Nov 28, 2012 at 9:15 AM, Martin Morgan <mtmorgan@fhcrc.org> wrote:

> 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
>
>
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-- 
*A model is a lie that helps you see the truth.*
*
*
Howard Skipper<http://cancerres.aacrjournals.org/content/31/9/1173.full.pdf>

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