Thanks for the link!
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Ming Tommy Tang
convert SNP calls to amino acid change
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
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2 answers
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
It looks like VEP can do this job: http://useast.ensembl.org/info/docs/tools/vep/vep_formats.html?redirect=no
Ming
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