Oncotator: Variant Type SNP/Type of Mutation

I am working on a project with several point mutations. I used oncotator to verify the type of mutation (ie. missense, nonsense, etc) and to see if they were unique mutations or SNPs. I received a variant type of SNP for each and every mutation, does that indeed mean that every mutation was a SNP or is this some type of default. I admit I am new to these databases and need clarification. I am also inquiring whether the indicated type of mutation is accurate...for most the type of mutation was consistent with oncotator, however, I received quite a few discrepancies indicating some of the mutations were splice sites or 3'UTR by oncotator.

Answers

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie

    Hi there,

    In this context, the term SNP is used here to describe all point mutations, regardless of whether they are unique or shared with other individuals.

    The consistency of annotations depends on the databases used. Since the databases are produced by others, we cannot guarantee their accuracy. If you see any significant discrepancies, feel free to check the source of the database entry.

  • KtangKtang Baltimore, MDMember

    Hi Dr. Auwera, I am looking for cosmic and dbnsp annotation data from Oncotator, in txt files that include annotations in format chromosome/start position/end position/reference allele/alternate allele so that I may match them with existing entries in our in-house mutation database. Are there links to download such databases and skip downloading the datasource corpus and oncotator? I am running Xubuntu in Linux. I appreciate your help.
    Sincerely
    Kenneth

  • LeeTL1220LeeTL1220 Arlington, MAMember, Broadie, Dev

    @Ktang Look in the datasources directory that you setup. I am assuming that you are talking about the standalone version and not the website.

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