If I create a GRanges object from a bam file that has been read in using ReadGappedAlignments and then another GRanges object from a list of SNPs, I can use findOverlaps to find those reads that overlap the SNPs in question, but not all of these reads will contain the SNP in question. For example, if the SNP is in a deletion contained within the read, it will return this read even though the SNP is not in the read. Can I make it return only reads that not only overlap the SNP but actually contain the SNP? Thank you. Eric -- output of sessionInfo(): not relevant -- Sent via the guest posting facility at bioconductor.org.

You probably want to turn your GAlignments into a GRangesList via grglist(ga, drop.D.ranges = TRUE). Michael On Fri, Jul 5, 2013 at 4:05 PM, Eric Foss [guest] <guest@bioconductor.org>wrote: > > If I create a GRanges object from a bam file that has been read in using > ReadGappedAlignments and then another GRanges object from a list of SNPs, I > can use findOverlaps to find those reads that overlap the SNPs in question, > but not all of these reads will contain the SNP in question. For example, > if the SNP is in a deletion contained within the read, it will return this > read even though the SNP is not in the read. Can I make it return only > reads that not only overlap the SNP but actually contain the SNP? > > Thank you. > > Eric > > > -- output of sessionInfo(): > > not relevant > > -- > Sent via the guest posting facility at bioconductor.org. > > _______________________________________________ > 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]]