How to consider/get the g. positions for variants in introns?

Question

[bioinfo89]

Hello All,

My query is regarding the genomic positions to be considered for a variant which are present in the intron.

For example: c.5278-1G>C, so the genomic position for c.5278 is 41203134.

Since the above nomenclature is 5278-1 which will be 5277th position and is the last base of the intron, can I consider (41203134-1) as its g. position?. I am not sure how to get the corresponding genomic positions in such cases.

I tried using Mutalyzer (position converter) but it throws error when I search. Can anyone suggest another tool or any R/Biocondutor package which can help in extraction of the corresponding g. position for variants in intron?

Thanks in advance.

Answer 1

[finswimmer]

Hello,

ensembl's VEP can do this. Along with the c. you have to provide a gene id, gene name or Transcript id. In case you not use a transcript id, be aware that the result can be ambiguous..

fin swimmer