SURVIVOR is a tool set for simulating/evaluating SVs, merging and comparing SVs within and among samples, and includes various methods to reformat or summarize SVs.

References:

• Transient structural variations have strong effects on quantitative traits and reproductive isolation in fission yeast. Jeffares, Daniel C; Jolly, Clemency; Hoti, Mimoza; Speed, Doug; Shaw, Liam; Rallis, Charalampos; Balloux, Francois; Dessimoz, Christophe; Bähler, Jürg; Sedlazeck, Fritz J. Nature communications, Vol. 8, 14061, 24.01.2017, p. 1-11. DOI:10.1038/NCOMMS14061

• SURVIVOR Main Site
• SURVIVOR wiki

• Module Name: survivor (see the modules page for more information)

Allocate an interactive session and run the program.
Sample session (user input in bold):

[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 survivor

[user@cn3144 ~]$ ls *vcf > sample-files
[user@cn3144 ~]$ SURVIVOR merge sample-files 1000 2 1 1 0 30 sample-merged.vcf

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

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

#!/bin/sh
set -e
module load survivor
SURVIVOR bincov lowMQ.cov 10 2 > lowMQ.bed

Submit this job using the Slurm sbatch command.

sbatch [--cpus-per-task=#] [--mem=#] survivor.sh

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

SURVIVOR merge sample1-files 1000 2 1 1 0 30 sample1-merged.vcf
SURVIVOR merge sample2-files 1000 2 1 1 0 30 sample2-merged.vcf
SURVIVOR merge sample3-files 1000 2 1 1 0 30 sample3-merged.vcf
SURVIVOR merge sample4-files 1000 2 1 1 0 30 sample4-merged.vcf

Submit this job using the swarm command.

swarm -f survivor.swarm [-g #] [-t #] --module survivor