Annotate a MAF File 📄

MAF files can be annotated using either the web interface or the command line client. The Mutation Mapper is a web-based tool and provides an easy-to-use graphical user interface for annotating MAF files. On the other hand, the command line client offers a more flexible approach for users who prefer command-line interfaces. Both options allow you to add additional information to the MAF file, which can be useful for downstream analysis and interpretation.

Annotate a MAF file using the command line client

To annotate a specific MAF file using the command line client, we will be using the genome-nexus-annotation-pipeline. This tool provides the options to customize the annotations according to your specific needs.

To use the genome-nexus-annotation-pipeline for annotations, the mutation data files must have at least five columns:

  • Chromosome

  • Start_Position

  • End_Position

  • Reference_Allele

  • Tumor_Seq_Allele1 or Tumor_Seq_Alele2

These essential columns provide the necessary information for accurate annotation of the variants.

Minimal Example

Create a MAF file:

(echo -e "Chromosome\tStart_Position\tEnd_Position\tReference_Allele\tTumor_Seq_Allele2"; 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

Reference Genome

The Genome Nexus Annotation Pipeline supports two versions of the human genome reference assembly: GRCh37 and GRCh38. By default, the pipeline uses GRCh37.

Using GRCh38

If you want to annotate with GRCh38, please set the GENOMENEXUS_BASE environment variable to Here's an example of how to do this:

docker run -e GENOMENEXUS_BASE= -v ${PWD}:/wd genomenexus/gn-annotation-pipeline:latest --filename /wd/input.txt  --output-filename /wd/output.txt --isoform-override uniprot

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