vcf2maf v1.6.16

vcf2maf converts a VCF into a MAF, where each variant is annotated to only one of all possible gene isoforms.

Accessing the software

To load the module:

$ module load vcf2maf/1.6.16-iomkl-2018a-Perl-5.26.0

vcf2maf requires access to Ensembl's VEP (Variant Effect Predictor), which is made available when the module command is executed.

An example command to include in your job script:

vcf2maf.pl --input-vcf test.vcf --output-maf test.maf --vep-path ${EBROOTVEP}

The location of your VEP cache should be specified by providing the --vep-data flag to vcf2maf.pl.

Accessing Previous Versions

Wherever possible, previous versions of this application will be retained for continuity, especially for research projects that require a consistent version of the software throughout the project. Such versions, however, may be unsupported by IT Services or the applications vendor, and may be withdrawn at short or no notice if they can no longer run on the cluster - for example, essential operating system upgrades may be incompatible with old versions.

At present there are no previous versions of this application on the BlueBEAR service.

Known Problems & Limitations

None.

Other Information

The Support Level for this application is An.

Visit the vcf2maf website for more information regarding this application.


Last modified: 12 July 2019