sniffles(1) structural variation caller for third-generation sequencing


sniffles -m string [-s int] [--max_num_splits int] [-q int][-l int] [-v string] [--bede string] [-c int] [-t int] [-d int] [-n int] [--use_MD_Cigar] [--] [--version] [-h]

sniffles -m reads.bam -v calls.vcf


Sniffles is a structural variation caller using third generation sequencing (PacBio or Oxford Nanopore). It detects all types of SVs using evidence from split-read alignments, high-mismatch regions, and coverage analysis. Please note the current version of Sniffles requires output from BWA-MEM with the optional SAM attributes enabled!


-m string, --mapped_reads string
(required) Bam File
-s int, --min_support int
Minimum number of reads that support a SV. Default: 10
--max_num_splits int
Maximum number of splits per read to be still taken into account. Default: 4
-q int, --minmapping_qual int
Minimum Mapping Quality. Default: 20
-l int, --min_length int
Minimum length of SV to be reported. Default:0
-v string, --vcf string
VCF output file name
--bede string
Simplified format of bede Format.
-c int, --min_cigar_event int
Minimum Cigar Event (e.g. Insertion, deletion) to take into account. Default:50
-t int, --threads int
Number of threads to use. Default: 3
-d int, --max_distance int
Maximum distance to group SV together. Default: 1kb
-n int, --num_reads_report int
Report up to N reads that support the SV. Default: 0
Enables Sniffles to use the alignment information to screen for suspicious regions.
--, --ignore_rest
Ignores the rest of the labeled arguments following this flag.
Displays version information and exits.
-h, --help
Displays usage information and exits.


If you experience problems or have suggestions please contact: [email protected]


Fritz Sedlazeck <[email protected]>.