NAME¶

sniffles - structural variation caller for third-generation sequencing data

SYNOPSIS¶

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] [--][--version] [-h] sniffles -m reads.bam -v calls.vcf

DESCRIPTION¶

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!

OPTIONS¶

-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

--, --ignore_rest

Ignores the rest of the labeled arguments following this flag.

--version

Displays version information and exits.

-h, --help

Displays usage information and exits.

BUGS¶

If you experience problems or have suggestions please contact: fritz.sedlazeck@gmail.com

SEE ALSO¶

bwa(1)

AUTHORS¶

Fritz Sedlazeck <fritz.sedlazech@gmail.com>.