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.
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