Maf files from GenomeNexus

[price0416]

We are considering switching fro VCF2MAF to GenomeNexus annotation tools.

GenomeNexus Annotation:

• Seems like it will generate standard VCF columns, but nothing else.
• Need to build annotation-pipeline JAR and then use annotation toolkit repo.
• They do not seem to have a docker containerized version of this toolkit, we would need to do that ourselves.
• Since the genomeNexus annotation tools suite only produces standard columns, we need a solution for other tempo generated column data.

System requirements:
• Java 8
• Maven
• Python 3

GitHub repos:
• genome-nexus-annotation-pipeline
• annotation-tools

Clone the annotation-tools GitHub repo

The annotation-tools directory will be your --annotation-scripts-home argument.

In a separate directory, clone the genome-nexus-annotation-pipeline GitHub repo and run mvn clean install

Copy annotationPipeline/target/*.jar to your --annotation-scripts-home location.

Refer to the annotation-tools README document for more details on what other input arguments are required and how to run the annotation tools:

Annotation Tools Readme

Relevant Links:
Mutation Annotation Format TCGAv2 - GDC Docs

File Format: MAF - GDC Docs

Genome Nexus Annotation Tool

Current VSF2MAF overview spreadsheet.

[rhshah]

Hi Adam, We are also looking for moving from vcf2maf, this definitely gives a window into GenomeNexus, is there a reason we cannot use API: https://www.genomenexus.org/swagger-ui.html#!/annotation45controller/fetchVariantAnnotationByGenomicLocationGET