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]]

