Question: How to convert mutation position from gene coordinate to genome coordinate?
0
gravatar for Alice
21 months ago by
Alice290
USA
Alice290 wrote:

I have a list of mutations coded as: GENE: c.1234
How do I convert to CHROM: g.1245364?

Is there a way, for example, to look them up in genome browser? I played with it a little bit, but could not find gene coordinate option.
Thanks in advance.

coordinate snp • 1.4k views
ADD COMMENTlink modified 21 months ago by bernatgel2.6k • written 21 months ago by Alice290
2
gravatar for bernatgel
21 months ago by
bernatgel2.6k
Barcelona, Spain
bernatgel2.6k wrote:

You should be able to do it with VEP (https://www.ensembl.org/info/docs/tools/vep/index.html), but beware of possible ambiguities if you only have the gene name but not the specific transcript. You might assume it refers to the "canonical" (usually the longest) transcript, but that's not always the case.

See also

Convert Cds-Based Coordinate To Genomic Coordinates

How to find the chromosomal coordinate of a mutation in a gene?

ADD COMMENTlink written 21 months ago by bernatgel2.6k
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