.TH "SNIFFLES" "1" "" "1.0.0" ""
.SH NAME
.PP
sniffles \- structural variation caller for third\-generation sequencing
data
.SH SYNOPSIS
.PP
\f[B]sniffles\f[] \-m \f[I]string\f[] [\-s \f[I]int\f[]]
[\-\-max_num_splits \f[I]int\f[]] [\-q \f[I]int\f[]][\-l \f[I]int\f[]]
[\-v \f[I]string\f[]] [\-\-bede \f[I]string\f[]] [\-c \f[I]int\f[]] [\-t
\f[I]int\f[]] [\-d \f[I]int\f[]] [\-n \f[I]int\f[]] [\-\-][\-\-version]
[\-h]
.PP
\f[B]sniffles\f[] \f[B]\-m\f[] \f[I]reads.bam\f[] \f[B]\-v\f[]
\f[I]calls.vcf\f[]
.SH DESCRIPTION
.PP
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!
.SH OPTIONS
.TP
.B \-m \f[I]string\f[], \-\-mapped_reads \f[I]string\f[]
(required) Bam File
.RS
.RE
.TP
.B \-s \f[I]int\f[], \-\-min_support \f[I]int\f[]
Minimum number of reads that support a SV.
Default: 10
.RS
.RE
.TP
.B \-\-max_num_splits \f[I]int\f[]
Maximum number of splits per read to be still taken into account.
Default: 4
.RS
.RE
.TP
.B \-q \f[I]int\f[], \-\-minmapping_qual \f[I]int\f[]
Minimum Mapping Quality.
Default: 20
.RS
.RE
.TP
.B \-l \f[I]int\f[], \-\-min_length \f[I]int\f[]
Minimum length of SV to be reported.
Default:0
.RS
.RE
.TP
.B \-v \f[I]string\f[], \-\-vcf \f[I]string\f[]
VCF output file name
.RS
.RE
.TP
.B \-\-bede \f[I]string\f[]
Simplified format of bede Format.
.RS
.RE
.TP
.B \-c \f[I]int\f[], \-\-min_cigar_event \f[I]int\f[]
Minimum Cigar Event (e.g.
Insertion, deletion) to take into account.
Default:50
.RS
.RE
.TP
.B \-t \f[I]int\f[], \-\-threads \f[I]int\f[]
Number of threads to use.
Default: 3
.RS
.RE
.TP
.B \-d \f[I]int\f[], \-\-max_distance \f[I]int\f[]
Maximum distance to group SV together.
Default: 1kb
.RS
.RE
.TP
.B \-n \f[I]int\f[], \-\-num_reads_report \f[I]int\f[]
Report up to N reads that support the SV.
Default: 0
.RS
.RE
.TP
.B \-\-, \-\-ignore_rest
Ignores the rest of the labeled arguments following this flag.
.RS
.RE
.TP
.B \-\-version
Displays version information and exits.
.RS
.RE
.TP
.B \-h, \-\-help
Displays usage information and exits.
.RS
.RE
.SH BUGS
.PP
If you experience problems or have suggestions please contact:
fritz.sedlazeck\@gmail.com
.SH SEE ALSO
.PP
\f[B]bwa\f[](1)
.SH AUTHORS
Fritz Sedlazeck <fritz.sedlazech@gmail.com>.