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VT on Biowulf and Helix

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


Running on Helix

Sample session:

helix$ module load vt
helix$ cd /data/$USER/dir
helix$ vt normalize dbsnp.vcf -r seq.fa -o dbsnp.normalized.vcf

# normalize variants and write out to dbsnp.normalized.vcf

Submitting a single batch job

1. Create a script file. The file will contain the lines similar to the lines below.

#! /bin/bash 
#SBATCH --mail-type=BEGIN,END,FAIL 

module load vt 
cd /data/$USER/vt 
vt normalize dbsnp.vcf -r seq.fa -o dbsnp.normalized.vcf
....
....

2. Submit the script on Biowulf.

$ sbatch myscript

see biowulf user guide for more options such as allocate more memory and longer walltime if needed.

Submit a swarm of jobs

Using the 'swarm' utility, one can submit many jobs to the cluster to run concurrently.

Set up a swarm command file (eg /data/$USER/cmdfile). Here is a sample file:

cd /data/user/run1/; vt normalize dbsnp.vcf -r seq.fa -o dbsnp.normalized.vcf
cd /data/user/run2/; vt normalize dbsnp.vcf -r seq.fa -o dbsnp.normalized.vcf
cd /data/user/run3/; vt normalize dbsnp.vcf -r seq.fa -o dbsnp.normalized.vcf
........

The -f flag is required to specify swarm file name.

Submit the swarm job:

$ swarm -f swarmfile --module vt

For more information regarding running swarm, see swarm.html

 

Running an interactive job

User may need to run jobs interactively sometimes. Such jobs should not be run on the Biowulf login node. Instead allocate an interactive node as described below, and run the interactive job there.

[user@biowulf]$ sinteractive 

[user@pXXXX]$ cd /data/$USER/myruns

[user@pXXXX]$ module load vt

[user@pXXXX]$ vt normalize dbsnp.vcf -r seq.fa -o dbsnp.normalized.vcf
[user@pXXXX]$ exit
slurm stepepilog here!
                   
[user@biowulf]$ 

Documentation

http://genome.sph.umich.edu/wiki/Vt#Normalization