VT is a variant tool set that discovers short variants from Next Generation Sequencing data.

References:

• http://bioinformatics.oxfordjournals.org/content/31/13/2202

• https://genome.sph.umich.edu/wiki/Vt#How_to_cite_vt.3F

• Module Name: vt (see the modules page for more information)
• Example files in /usr/local/apps/vt/version/test

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

[user@biowulf]$ sinteractive
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 vt
[user@cn3144 ~]$ vt normalize IN.vcf -r ref.fa -o out.vcf

[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

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

#!/bin/bash
set -e
module load vt
vt normalize IN.vcf -r ref.fa -o out.vcf

Submit this job using the Slurm sbatch command.

sbatch batch.sh

Create a swarmfile (e.g. job.swarm). For example:

cd dir1; vt normalize IN.vcf -r ref.fa -o out.vcf
cd dri2; vt normalize IN.vcf -r ref.fa -o out.vcf
cd dir3; vt normalize IN.vcf -r ref.fa -o out.vcf

Submit this job using the swarm command.

swarm -f job.swarm [-g #] [-t #] --module vt