map cDNA position on genomic position

Question

[User6891]

Hi everyone,

I have a list of cDNA positions from mutations. Is there a tool with which I can convert this cDNA position to the genomic location?

Thanks in advance

[Ram]

Interesting question. I know how to get to genomic from protein muts, but not from cDNA. Following this post now.

[cwwong13]

Hi @Ram, Would you mind sharing how to get to genomic coordinates from protein mutation?

[Ram]

I think Pierre Lindenbaum's BackLocate is one of the easiest ways to do that. Other than that, one might need to use esearch on dbSNP or the python hgvs module. It's been a while so my memory is quite rusty on this topic.

Answer 1

[Denise CS]

Do you know the transcripts IDs these mutations were mapped to? If so, you may want to try the Ensembl REST API to covert the cDNA to genomic coordinates. If your list consist of mutations under the HGVS notations, you can also use the VEP. One of the results (among many others) of VEP will be the genomic location of those mutations.