Convert Cds-Based Coordinate To Genomic Coordinates

Question

[Luca Beltrame]

I was given a list of loci of interest for a particular gene, which contain mutations: unfortunately, all the information are using local base coordinates, while I'm in need to retranslate them to genomic coordinates to perform some additional work in preparation for validation. I've seen a few example of genomic -> local coordinate transformation, but not the opposite.

Bear in mind that I have access to the whole annotation of the genome (Homo sapiens), so using additional files and/or resources wouldn't be a problem.

Is there a way to convert from local coordinates to genomic coordinates? Python or R solutions would be preferred.

[Pierre Lindenbaum]

which organism ?

[Luca Beltrame]

It's Homo sapiens.

[Irsan]

Is this the problem where you have variants reported on transcript level like g.195insCTGATA in RB1 gene? Having the same problem here... I am looking forward to Pierre's solution

[Luca Beltrame]

More like genomic sequence (all the coordinates are mapped to the canonical variant of the gene), but yes, something like that.

Answer 1

[Emily]

Ensembl REST API. Scroll down to Mapping to see tools to get genomic coordinates from cDNA, CDS and protein coordinates. Since it's a REST API, you can use it in your favourite language.