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

Valerie Obenchain vobencha at fhcrc.org
Thu Dec 19 04:08:19 CET 2013


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.


> 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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