SNIFFLES

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 DOT sedlazech AT gmail DOT com>.