sniffles on Biowulf

Sniffles is a structural variation caller using third generation sequencing (PacBio or Oxford Nanopore). It detects all types of SVs (10bp+) using evidence from split-read alignments, high-mismatch regions, and coverage analysis. Please note the current version of Sniffles requires sorted output from BWA-MEM (use -M and -x parameter) or NGMLR with the optional SAM attributes enabled


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 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 sniffles
[+] Loading sniffles, version 2.0.2...
[user@cn3144 ~]$ sniffles -i /fdb/sniffles/reads_region.bam -v test.vcf
Estimating parameter...
Max dist between aln events: 4
Max diff in window: 50
Min score ratio: 2
Avg DEL ratio: 0.0432235
Avg INS ratio: 0.0740733
Start parsing... 21
Switch Chr 21
Finalizing  ..
[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. For example:

set -e
module load sniffles
sniffles -i /fdb/sniffles/reads_region.bam -v test.vcf

Submit this job using the Slurm sbatch command.

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

sniffles -i sample1.bam -v sample1.vcf --threads $SLURM_CPUS_PER_TASK
sniffles -i sample2.bam -v sample2.vcf --threads $SLURM_CPUS_PER_TASK
sniffles -i sample3.bam -v sample3.vcf --threads $SLURM_CPUS_PER_TASK
sniffles -i sample4.bam -v sample4.vcf --threads $SLURM_CPUS_PER_TASK

Submit this job using the swarm command.

swarm -f sniffles.swarm [-g #] -t 4 --module sniffles
-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 sniffles Loads the sniffles module for each subjob in the swarm