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

[Robert Castelo]

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)


thanks!!
robert.