Hi,

I was wondering if anyone knows if there is a default protein database linked to the MAF files of the TCGA project?

Basically what I want to do is to get the mutated protein sequences that correspond to the missense mutations listed in the MAF files. For that, I need the correct protein sequence for each gene with a missense mutation, since the MAF file has the position of the mutation in the gene and in the protein, I can write a simple script that changes the wild type amino acid with the mutation. However, it is crucial to get the correct protein sequence, so that the position and wild type amino acid stored in the MAF file corresponds to the same amino acid in that position of the protein sequence in the database.

Thanks
The latest TCGA MAF standard is to choose the "[worst affected][1]" isoform per variant, from among the Gencode Basic v19 isoforms. These standards have changed over time, so not all MAFs will use the same isoform database. You'll find GAF files listed [here][2], originally based on UCSC KnownGenes, but now based on Gencode Basic v19.

If you want to map each variant to [Uniprot's canonical isoform][3] per gene, then pull the Ensembl ENST IDs of all Uniprot's canonical isoforms, dump them into a text file one ID per line, and pass it to [maf2maf][4] under argument `--custom-enst`, to re-annotate all TCGA MAFs.

 [1]: http://useast.ensembl.org/info/genome/variation/predicted_data.html#consequences
 [2]: https://tcga-data.nci.nih.gov/docs/GAF/
 [3]: http://www.uniprot.org/help/canonical_and_isoforms
 [4]: https://github.com/ckandoth/vcf2maf