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Svtyper on Biowulf and Helix

Svtyper is a Bayesian genotyper for structural variants.

Example dataset can be copied from /usr/local/apps/svtyper/testdata directory

Running on Helix

Sample session:

helix$ module load svtyper
helix$ cd /data/$USER/dir
helix$ zcat NA12878.20.vcf.gz
helix$ svtyper -B NA12878.20.bam -S NA12878.20.splitters.bam > NA12878.20.gt.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 svtyper 
cd /data/$USER/svtyper 
svtyper -B NA12878.20.bam -S NA12878.20.splitters.bam > NA12878.20.gt.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/; svtyper -B NA12878.20.bam -S NA12878.20.splitters.bam > NA12878.20.gt.vcf
cd /data/user/run2/; svtyper -B NA12878.20.bam -S NA12878.20.splitters.bam > NA12878.20.gt.vcf
cd /data/user/run3/; svtyper -B NA12878.20.bam -S NA12878.20.splitters.bam > NA12878.20.gt.vcf
........

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

Submit the swarm job:

$ swarm -f swarmfile --module svtyper

- Use -g flag for more memory (default 1.5gb per line in swarmfile)

- Use --time flag for longer walltime

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 svtyper

[user@pXXXX]$ svtyper -B NA12878.20.bam -S NA12878.20.splitters.bam > NA12878.20.gt.vcf
[user@pXXXX]$ exit
slurm stepepilog here!
                   
[user@biowulf]$ 

Documentation

https://github.com/hall-lab/svtyper