Question

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

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wang peter ★ 2.0k

@wang-peter-4647

Last seen 10.2 years ago

this function can be realized by bcftools but those tools have some problems thank you -- shan gao Room 231(Dr.Fei lab) Boyce Thompson Institute Cornell University Tower Road, Ithaca, NY 14853-1801 Office phone: 1-607-254-1267(day) Official email:sg839 at cornell.edu Facebook:http://www.facebook.com/profile.php?id=100001986532253

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ADD COMMENT • link updated 12.0 years ago by Martin Morgan 25k • written 12.0 years ago by wang peter ★ 2.0k

score 0 · Answer 1 · 2012-11-28

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Martin Morgan 25k

@martin-morgan-1513

Last seen 4 months ago

United States

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

ADD COMMENT • link 12.0 years ago Martin Morgan 25k

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> 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 > > > ______________________________**_________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/**listinfo/bioconductor<https: stat.et="" hz.ch="" mailman="" listinfo="" bioconductor=""> > Search the archives: http://news.gmane.org/gmane.** > science.biology.informatics.**conductor<http: news.gmane.org="" gmane.="" science.biology.informatics.conductor=""> > -- *A model is a lie that helps you see the truth.* * * Howard Skipper<http: cancerres.aacrjournals.org="" content="" 31="" 9="" 1173.full.pdf=""> [[alternative HTML version deleted]]