How to transform genomic coordinates into mature mRNA positions?

Question

[Firingam]

Hi, I have been analyzing some cancer mutations in different mRNA. We focused on missense and synonymous mutations, so we have been focused on those mutations falling on protein-coding regions of our genes. Mutations are annotated with genomic positions, so positions represent chromosome positions. My question is how to transform these in mature mRNA positions so that I will be able to know, in the case of missense mutations, which amino acid will be changed. I really appreciate any help you can provide.

Answer 1

[colindaven]

This is an exhaustively discussed topic.

Representative AA change from point mutation given by genomic lcus

• ensembl VEP
• SNPeff
• annovar etc