Converting HGVS cDNA notations to chromosome position

Question

[pastatonio78]

Hi,

I would like to automate the conversion of cDNA notations to chromosome position by using a batch request web service or some kind of API (ideally in R, but I am open to other languages).

The perfect tool would to get the anchor nucleotide and position for INDEL, for example:

NM_000059.3:c.3847_3848delGT --> 13:32912339_TGT>GT

I already tried VEP from Ensembl, but it doesnt give satisfactory results.

Thanks for your suggestions

Antoine

Answer 1

[Atu]

There are several libraries to work with hgvs ids. You may check the hgvs python library for mapping IDs to genomic coordinates:

http://hgvs.readthedocs.org/en/0.4.x/reference.html