sniffles - structural variation caller for third-generation
sequencing data
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
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
- –, –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.
If you experience problems or have suggestions please contact:
fritz.sedlazeck@gmail.com
Fritz Sedlazeck <fritz.sedlazech@gmail.com>.