vcf2maf
Link to section 'Introduction' of 'vcf2maf' Introduction
To convert a VCF into a MAF, each variant must be mapped to only one of all possible gene transcripts/isoforms that it might affect. This selection of a single effect per variant, is often subjective. So this project is an attempt to make the selection criteria smarter, reproducible, and more configurable. And the default criteria must lean towards best practices.
Home page: https://github.com/mskcc/vcf2maf
Link to section 'Versions' of 'vcf2maf' Versions
- 1.6.21
Link to section 'Commands' of 'vcf2maf' Commands
- maf2maf.pl
- maf2vcf.pl
- vcf2maf.pl
- vcf2vcf.pl
Link to section 'Module' of 'vcf2maf' Module
You can load the modules by:
module load biocontainers
module load vcf2maf
Link to section 'Example job' of 'vcf2maf' Example job
Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.
If users need to use vep, please add --vep-path /opt/conda/bin.
To run vcf2maf on our clusters:
#!/bin/bash
#SBATCH -A myallocation # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=vcf2maf
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
ml biocontainers vcf2maf
vcf2maf.pl --vep-path /opt/conda/bin \
--ref-fasta Homo_sapiens.GRCh37.dna.toplevel.fa.gz \
--input-vcf tests/test.vcf --output-maf test.vep.maf