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>.