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sniffles website  

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 NGM-LR with the optional SAM attributes enabled!

Environment Modules

Run module spider sniffles to find out what environment modules are available for this application.

System Variables

  • HPC_SNIFFLES_DIR - installation directory
  • HPC_SNIFFLES_BIN - executable directory


If you publish research that uses sniffles you have to cite it as follows:

Accurate detection of complex structural variations using single molecule sequencing