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

References:

• Accurate detection of complex structural variations using single-molecule sequencing. Fritz J. Sedlazeck, Philipp Rescheneder, Moritz Smolka, Han Fang, Maria Nattestad, Arndt von Haeseler & Michael C. Schatz. Nature Methods volume 15, 461–468 (2018). [html]

• sniffles Main Site

• Module Name: sniffles (see the modules page for more information)
• Example files in /fdb/sniffles
• sniffles uses 4 threads by default. Specify --threads and allocate the corresponding number of threads with your job submission.

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 ~]$

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

#!/bin/sh
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=#] sniffles.sh

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