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
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]
Documentation
Important Notes
- 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.
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. 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
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 sniffleswhere
| -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 |