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
