Hi All I want to extract the genomic locations of insertions and deletions of aligned reads. In the BAM file, I identify the insertions/deletions from the cigar string. However I would need to translate this cigar string into genomic coordinates. From reading the documentation, it seems that the method GenomicRanges::queryLoc2refLoc would be the suitable method. The documentation says: > For|queryLoc2refLoc|: An integer vector of the same length > as|qloc|containing the "reference-based locations" (i.e. the 1-based > locations relative to the reference sequence) corresponding to the > "query-based locations" passed in|qloc|. > > Unfortunately it is not yet implemented. Would there be another option or a workaround? Best regards Hubert [[alternative HTML version deleted]]

Please see the devel version of VariantTools. Pass indels=TRUE to TallyVariantsParam; see the vignette. You can use it now, but be aware there will be some tweaks in upcoming version 1.3.8. Also, for the record, there is a hidden function prmap in GenomicRanges that given a set of read/query Ranges and a GAlignments outputs an IRanges of reference locations (obviously assumed to be on the same chromosome as the alignment). Just haven't had time to test/document it, etc. On Wed, Sep 11, 2013 at 9:45 PM, Hubert Rehrauer < Hubert.Rehrauer@fgcz.ethz.ch> wrote: > Hi All > > I want to extract the genomic locations of insertions and deletions of > aligned reads. In the BAM file, I identify the insertions/deletions from > the cigar string. However I would need to translate this cigar string > into genomic coordinates. > > From reading the documentation, it seems that the method > GenomicRanges::queryLoc2refLoc would be the suitable method. The > documentation says: > > > For|queryLoc2refLoc|: An integer vector of the same length > > as|qloc|containing the "reference-based locations" (i.e. the 1-based > > locations relative to the reference sequence) corresponding to the > > "query-based locations" passed in|qloc|. > > > > > Unfortunately it is not yet implemented. Would there be another option > or a workaround? > > Best regards > Hubert > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]