vcf2maf on Biowulf

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.

Important Notes

Interactive job
Interactive jobs should be used for debugging, graphics, or applications that cannot be run as batch jobs.

Allocate an interactive session and run the program. Sample session:

[user@biowulf]$ sinteractive --cpus-per-task=8 --mem=20g
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job

[user@cn3144 ~]$ module load VEP/106 vcf2maf

[user@cn3144 ~]$ rm -rf test_{vcf2maf,maf2maf,maf2vcf}
[user@cn3144 ~]$ mkdir test_vcf2maf && cd $_
[user@cn3144 ~]$ cp  $VCF2MAF_EXAMPLES/test.vcf .
[user@cn3144 ~]$ \
  --input-vcf test.vcf \
  --output-maf test.maf \
  --vep-path $VEP_HOME/bin \
  --vep-data $VEP_CACHEDIR \
  --ref-fasta $VEP_CACHEDIR/GRCh38.fa \
  --ncbi-build GRCh38 \
  --cache-version $VEP_VERSION \
  --vep-forks ${SLURM_CPUS_ON_NODE:-2} \
[user@cn3144 ~]$ cd ..

[user@cn3144 ~]$ mkdir test_maf2maf && cd $_
[user@cn3144 ~]$ cp $VCF2MAF_EXAMPLES/test.maf .
[user@cn3144 ~]$ \
  --input-maf test.maf \
  --output-maf test.vep.maf \
  --ref-fasta $VEP_CACHEDIR/GRCh37.fa \
  --vep-path $VEP_HOME/bin \
  --vep-data $VEP_CACHEDIR
[user@cn3144 ~]$ cd ..

[user@cn3144 ~]$ mkdir test_maf2vcf && cd $_
[user@cn3144 ~]$ cp $VCF2MAF_EXAMPLES/test.maf .
[user@cn3144 ~]$ \
  --input-maf test.maf \
  --output-dir vcfs \
  --ref-fasta $VEP_CACHEDIR/GRCh37.fa

Batch job
Most jobs should be run as batch jobs.

Create a batch input file (e.g. For example:

module load VEP/106 vcf2maf --input-vcf /path/to/data/test.vcf --output-maf test.maf --vep-path $VEP_HOME/bin --vep-data $VEP_CACHEDIR --cache-version $VEP_VERSION \
  --ref-fasta $VEP_CACHEDIR/GRCh38.fa --ncbi-build GRCh38 --vep-forks $SLURM_CPUS_ON_NODE

Submit this job using the Slurm sbatch command.

sbatch [--cpus-per-task=#] [--mem=#]
Swarm of Jobs
A swarm of jobs is an easy way to submit a set of independent commands requiring identical resources.

Create a swarmfile (e.g. vcf2maf.swarm). For example: --input-vcf data/test1.vcf --output-maf data/test1.maf --vep-path $VEP_HOME/bin --vep-data $VEP_CACHEDIR --cache-version $VEP_VERSION --ref-fasta $VEP_CACHEDIR/GRCh38.fa --ncbi-build GRCh38 --vep-forks $SLURM_CPUS_ON_NODE --input-vcf data/test2.vcf --output-maf data/test2.maf --vep-path $VEP_HOME/bin --vep-data $VEP_CACHEDIR --cache-version $VEP_VERSION --ref-fasta $VEP_CACHEDIR/GRCh38.fa --ncbi-build GRCh38 --vep-forks $SLURM_CPUS_ON_NODE --input-vcf data/test3.vcf --output-maf data/test3.maf --vep-path $VEP_HOME/bin --vep-data $VEP_CACHEDIR --cache-version $VEP_VERSION --ref-fasta $VEP_CACHEDIR/GRCh38.fa --ncbi-build GRCh38 --vep-forks $SLURM_CPUS_ON_NODE --input-vcf data/test4.vcf --output-maf data/test4.maf --vep-path $VEP_HOME/bin --vep-data $VEP_CACHEDIR --cache-version $VEP_VERSION --ref-fasta $VEP_CACHEDIR/GRCh38.fa --ncbi-build GRCh38 --vep-forks $SLURM_CPUS_ON_NODE

Submit this job using the swarm command.

swarm -f vcf2maf.swarm [-g #] [-t #] --module vcf2maf VEP/106
-g # Number of Gigabytes of memory required for each process (1 line in the swarm command file)
-t # Number of threads/CPUs required for each process (1 line in the swarm command file).
--module vcf2maf Loads the vcf2maf module for each subjob in the swarm