convert SNP calls to amino acid change

Question

[Ming Tommy Tang]

I am wondering if I have a maf file describing the snps, how can I easily convert it to amino acid changes.

Missense_Mutation 23 66937331 66937331 T A -> L729I

I know I can grab the sequences around the mutation point (also needs to know where is the start codon),

and use the triplets table to find it out the changes.

I just want to know if there is an existing tool for that.

Thanks,
Ming

Answer 1

[cpad0112]

Roundabout way is to

• Convert MAF file to VCF. Tutorial is given here: Annotating TCGA MAFs with the latest Ensembl/Gencode transcripts
• Run VEP (ensembl), Variation reporter (NCBI), SNPeff on converted VCF and output as VCF
• Convert VCF back to MAF. Tutorial is given here: Annotating TCGA MAFs with the latest Ensembl/Gencode transcripts

[Ming Tommy Tang]

Thanks for the link!

Answer 2

[Ming Tommy Tang]

It looks like VEP can do this job: http://useast.ensembl.org/info/docs/tools/vep/vep_formats.html?redirect=no

Ming