VCF2MAF

 

VCF2MAF converts a VCF into a MAF, where each variant is annotated to only one of all possible gene isoforms.

Documentation

 

Usage

To see what versions of vcf2maf are available type

module avail vcf2maf

To see what other modules are needed, what commands are available and how to get additional help type

module help vcf2maf

For more help and links to more documentation, load the modules recommended by the module help vcf2maf command and then type 

perl $VCF2MAF_HOME/vcf2maf.pl --man

To use vcf2maf, include a command like this in your batch script or interactive session to load the vcf2maf module:

module load vcf2maf

Be sure you also load any other modules needed, as listed by the module help vcf2maf command.