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Annotate a MAF File 📄

You can use either the web interface or the command line client to annotate a MAF

Annotate a MAF file using the command line client

We will be using the genome-nexus-annotation-pipeline for this.

Minimal Example

Create a MAF file:
(echo -e "Chromosome\tStart_Position\tEnd_Position\tReference_Allele\tTumor_Seq_Allele1"; echo -e "7\t55220240\t55220240\tG\tT") > input.txt;
Run the annotator using docker:
docker run -v ${PWD}:/wd genomenexus/gn-annotation-pipeline:master --filename /wd/input.txt --output-filename /wd/output.txt --isoform-override uniprot
Output can be found in output.txt