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