oncokb-annotator

Annotates variants in MAF with OncoKB annotation.

Please try

python MafAnnotator.py -h
python FusionAnnotator.py -h
python CnaAnnotator.py -h
python ClinicalDataAnnotator.py -h
python OncoKBPlots.py -h

Example input files are under data. An example script is here: example.sh

We recommend processing MAF files by vcf2maf with MSK override isoforms before using the MafAnnotator here.

FAQs

How to get the subversion of the ensembl transcript ID?
vcf2maf is designed to work with all Ensembl releases and reference genomes, that is the reason the subversion is not included.

Within MSK, we are using GRCh37 which corresponding to the Ensembl release 75. You can get the full list of versioned transcript IDs here http://grch37.ensembl.org/biomart/martview/40d921c6ab6956144cf6fb2e9a8ca093?VIRTUALSCHEMANAME=default&ATTRIBUTES=hsapiens_gene_ensembl.default.feature_page.ensembl_transcript_id_version&FILTERS=&VISIBLEPANEL=attributepanel.