[BioC] Complete variant toolbox: gmapR/VariantTools/VariantAnnotation

[Thomas Girke]

Sorry for not responding sooner. - I agree, providing the variant mapping
position relative to transcripts will be the most useful one, at least
for features that are part of transcripts. For others that are not, e.g.
intron and intergenic features, one could report the variant mappings
relative to the start position of these features.

Thomas

On Thu, Dec 19, 2013 at 03:08:19AM +0000, Valerie Obenchain wrote:
> Hi,
> 
> On 12/17/2013 09:40 AM, Robert Castelo wrote:
> > hi Valerie cc Thomas,
> >
> > sorry for hijacking the thread, regarding the request made below..
> >
> > On 12/09/2013 09:07 PM, Valerie Obenchain wrote:
> > [...]
> >> I could add a 'REFLOC' column to the otuput of locateVariants() that
> >> would essentially be the "equivalent" to 'CDSLOC' from predictCoding().
> >
> > for the purpose of ordering cDNA primers flanking variants which one may
> > want to validate through sanger sequencing, it is useful to have at hand
> > the position of the variant with respect to the beginning of the
> > transcript (cDNA) where it has been observed, thus not just from the
> > beginning of the CDS but from the beginning of the transcript.
> >
> > is this newer 'REFLOC' going to contain this position? if not, would it
> > be possible to get also a column for that from the locateVariants()
> > call? (e.g., TXLOC)
> 
> Yes, I think it makes sense to have 'REFLOC' be the position in the 
> reference starting from the beginning of the transcript. Unless others 
> have different thoughts this is what I'll go ahead with.
> 
> Valerie
> 
> 
> 
> 
> 
> >
> >
> > thanks!!
> > robert.
> 
> 
> -- 
> Valerie Obenchain
> 
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N, M1-B155
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> 
> E-mail: vobencha at fhcrc.org
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