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), Minimap2 (sam file with Cigar & MD string) or NGMLR.

• Version: 1.0.12b
• Added: August, 2020
• Link: https://github.com/fritzsedlazeck/Sniffles

See versions of sniffles which are available:

$ module avail sniffles

Load one version into your environment and run it:

$ module load sniffles/1.0.12b
$ sniffles

Notes from the sysadmin during installation:

$ cd /tmp
$ wget https://github.com/fritzsedlazeck/Sniffles/archive/v1.0.12b.tar.gz
$ tar xf v1.0.12b.tar.gz
$ cd Sniffles-1.0.12b
$ mkdir -p build/
$ cd build/
$ cmake ..
$ make
$ sudo mkdir -p /export/apps/sniffles/1.0.12b/bin
$ sudo cp ../bin/sniffles-core-1.0.12/sniffles /export/apps/sniffles/1.0.12b/bin