Thanks, all. Choice is a good thing. Sean
On Fri, Feb 14, 2014 at 8:02 AM, Michael Lawrence <lawrence.mich...@gene.com > wrote: > If we're listing alternative solutions, then there's > VariantTools::tallyVariants. > > > On Fri, Feb 14, 2014 at 12:28 AM, Julian Gehring <julian.gehr...@embl.de > >wrote: > > > Hi Sean, > > > > You can have a look at the 'bam2R' function from the 'deepSNV' package. > > This will extract the base/insertion/deletion counts, base call > qualities, > > and other metrics strand-specific from a BAM file. > > > > Best wishes > > Julian > > > > > > > > On 13/02/14 17:09, Sean Davis wrote: > > > >> Hi, Martin. > >> > >> How difficult would it be to include insertions/deletions in seq and > qual > >> in the applyPileups method for PileupFiles? The use case is to look at > >> the > >> context around variants for increases mismatch rates. Indels will have > a > >> small impact on such calculations, but for completeness it would be nice > >> to > >> have. > >> > >> Thanks, > >> Sean > >> > >> [[alternative HTML version deleted]] > >> > >> _______________________________________________ > >> Bioc-devel@r-project.org mailing list > >> https://stat.ethz.ch/mailman/listinfo/bioc-devel > >> > >> > > _______________________________________________ > > Bioc-devel@r-project.org mailing list > > https://stat.ethz.ch/mailman/listinfo/bioc-devel > > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
