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MAF Annotation
Yichao Sun edited this page Jul 3, 2018
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A maf is not annotated if "HGVSp_short" column does not exist in the MAF.
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Make sure the MAF follows file format and has the required columns https://github.com/cbioportal/cbioportal/blob/master/docs/File-Formats.md#mutation-data
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Run the MAF clean up tool on the MAF before annotation: https://github.com/cBioPortal/datahub-study-curation-tools/tree/master/maf_cleanup
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For annotation, simply run the annotator jar using the command line below. The annotator jar could be found on dashi-dev under /data/curation/annotation/ (ISOFORM is mskcc or uniprot)
java -jar annotationPipeline-0.1.0.jar --filename MAF_FILE_TO_BE_ANNOTATED --output-filename OUTPUT_MAF_FILE --isoform-override ISOFORM
- A detailed log called annotator.log would be generated separately from the annotator.