On Thu, Feb 13, 2014 at 1:12 PM, Martin Morgan <mtmor...@fhcrc.org> wrote:
> On 02/13/2014 08:09 AM, 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. >> > > Actually we're in the process of revisiting how pileups are calculated, so > it's a great time to express what you'd like. Are you asking for > per-position information on indel occurrence? > Thanks, Martin. For my particular use case, simply including the insertions and deletions covering a position in the seq and qual returned from applyPileup would be good enough. I don't know if there are more interesting cases that would require more detail about the insertion or deletion, though. Sean > > >> Thanks, >> Sean >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioc-devel@r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/bioc-devel >> >> > > -- > Computational Biology / Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N. > PO Box 19024 Seattle, WA 98109 > > Location: Arnold Building M1 B861 > Phone: (206) 667-2793 > > _______________________________________________ > 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
