Provided by: sniffles_1.0.11+ds-1_amd64
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: firstname.lastname@example.org
Fritz Sedlazeck <email@example.com>.