On Thu, Nov 3, 2011 at 11:42 AM, Valerie Obenchain <vobencha@fhcrc.org>wrote: > Michael, > > Is globalToQuery similar to globalToLocal in VariantAnnotation? It looks > like a C implementation of the same idea ...? > > > It's a similar idea but globalToQuery parses a cigar string to handle things like insertions. I think both could use the map() generic. globalToLocal() is between a GRanges and a GRangesList or something. > Alpesh, > > You may also want to check out these functions from the VariantAnnotaiton > package, > ?globalToLocal > ?predictCoding > > > Valerie > > > > On 11/03/2011 11:22 AM, Michael Lawrence wrote: > >> There is a function inside GenomicRanges that maps from global positions >> to >> read positions, considering the cigar. I have not exported it yet, because >> I want the output (the mapping) to have a formal class, like >> RangesMapping. >> Haven't had time to do that yet. Anyone want to pick it up for me? Also, I >> think we should use a generic for this, perhaps map() that does this when >> given a GRanges (of variants) and a GappedAlignments (reads). >> >> Anyway, it is here: >> GenomicRanges:::globalToQuery. >> >> YMMV. >> >> Michael >> >> On Thu, Nov 3, 2011 at 10:54 AM, Alpesh Querer<alpeshq@gmail.com> wrote: >> >> Hi All, >>> >>> I want to know if there is a way to extract variant nucleotide(s) from >>> reads >>> that align to particular locations. This should also take care of the >>> soft/hard clips, split alignments etc. >>> I have a filtered BAM file with reads which cover my loci of interest. >>> For >>> example an an insertion GAA >>> exists in the reference at ch1:1234-1236. I want to tabulate all variant >>> alleles at ch1:1234-1236. >>> >>> Thanks, >>> Alpesh >>> >>> [[alternative HTML version deleted]] >>> >>> ______________________________**_________________ >>> Bioconductor mailing list >>> Bioconductor@r-project.org >>> https://stat.ethz.ch/mailman/**listinfo/bioconductor<https: stat.="" ethz.ch="" mailman="" listinfo="" bioconductor=""> >>> Search the archives: >>> http://news.gmane.org/gmane.**science.biology.informatics.**conduc tor<http: news.gmane.org="" gmane.science.biology.informatics.conductor=""> >>> >>> [[alternative HTML version deleted]] >> >> ______________________________**_________________ >> Bioconductor mailing list >> Bioconductor@r-project.org >> https://stat.ethz.ch/mailman/**listinfo/bioconductor<https: stat.e="" thz.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=""> >> > > ______________________________**_________________ > 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=""> > [[alternative HTML version deleted]]