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