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vatlab / vat-docs

Documentation for Variant Tools.
https://vatlab.github.io/vat/
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Use.md #32

Open jma7 opened 4 years ago

jma7 commented 4 years ago 
% vtools use CancerGeneCensus --linked_fields kgID --linked_by knownGene.name
    INFO: Choosing version CancerGeneCensus-20170912 from 4 available databases.
    INFO: Downloading annotation database annoDB/CancerGeneCensus-20170912.ann
    INFO: Using annotation DB CancerGeneCensus as CancerGeneCensus in project use.
    INFO: This database contains variants from the Cancer Genome Project. It is
    an ongoing effort to catalogue those genes for which mutations have been causally
    implicated in cancer. The original census and analysis was published in Nature
    Reviews Cancer and supplemental analysis information related to the paper is also
    available. Currently, more than 1% of all human genes are implicated via mutation
    in cancer. Of these, approximately 90% have somatic mutations in cancer, 20% bear
    germline mutations that predispose to cancer and 10% show both somatic and
    germline mutations.
    INFO: 0 out of 197782 knownGene.knownGene.name are annotated through annotation database CancerGeneCensus