I am working on a TCGA breast cancer dataset and wanted to check the prevalence of a specific mutation in this population. If I found an interested mutation from COSMIC, I am wondering how I can link or screen this COSMIC ID (e.g. COSM43759) in the TCGA population. Does somebody have experiences on this analysis?
You can normally view this type of information on cBioPortal, which includes COSMIC IDs, however, as your mutation is intronic, it's not actually included. To normally view these, go here and select your gene. You'll then see a page that has COSMIC as a heading.
If I were you, I would take the time to set-up a 'local' Rdata file that contained all of the mutation data, and then you can look up your mutations with ease. You can download the BRCA TCGA mutation data in MAF format from the GDC Legacy archive.