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
>
>
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