Biowulf High Performance Computing at the NIH
SV2 on Biowulf

From the SV2 documentation:

SV2 filters and integrates structural variants from multiple calling algorithms. Given multiple samples, SV2 creates a genotype matrix. SV2 also provides annotations for genes, repeat elements, and common SVs for filtering post-genotyping.

References:

  • D. Antaki, W. M. Brandler and J. Sebat. SV2: Accurate Structural Variation Genotyping and De Novo Mutation Detection from Whole Genomes Bioinformatics 34: 1774-1777 (2018) PubMed |  PMC |  Journal
Documentation
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
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 sv2
[user@cn3144]$ sv2 -i in.bam -v sv.vcf -snv in.vcf.gz -p in.ped

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

Batch job
Most jobs should be run as batch jobs.

Create a batch input file (e.g. sv2.sh), which uses the input file 'sv2.in'. For example:

#!/bin/bash
module load sv2/1.4.3.4
sv2 -i in.bam -v sv.vcf -snv in.vcf.gz -p in.ped

Submit this job using the Slurm sbatch command.

sbatch [--cpus-per-task=#] [--mem=#] sv2.sh
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. sv2.swarm). For example:

sv2 -i in1.bam -v sv1.vcf -snv in1.vcf.gz -p in.ped
sv2 -i in2.bam -v sv2.vcf -snv in2.vcf.gz -p in.ped

Submit this job using the swarm command.

swarm -f sv2.swarm [-g #] [-t #] --module sv2
where
-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 sv2 Loads the sv2 module for each subjob in the swarm