Svtyper is a Bayesian genotyper for structural variants.

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

• https://github.com/hall-lab/svtyper

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

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 svtyper
[user@cn3144 ~]$ svtyper -B NA12878.20.bam -S NA12878.20.splitters.bam > NA12878.20.gt.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 svtyper
svtyper -B NA12878.20.bam -S NA12878.20.splitters.bam > NA12878.20.gt.vcf

Submit this job using the Slurm sbatch command.

sbatch [--mem=#] batch.sh

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

cd dir1; svtyper -B NA12878.20.bam -S NA12878.20.splitters.bam > NA12878.20.gt.vcf
cd dir2; svtyper -B NA12878.20.bam -S NA12878.20.splitters.bam > NA12878.20.gt.vcf
cd dir3; svtyper -B NA12878.20.bam -S NA12878.20.splitters.bam > NA12878.20.gt.vcf

Submit this job using the swarm command.

swarm -f job.swarm [-g #] --module svtyper