.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.8.
.TH KISSNP2 "1" "January 2019" "kissnp2 2.3.0" "User Commands"
.SH NAME
kissnp2 \- detects SNPs and indels from read sets
.SH DESCRIPTION
[Kissnp2 options]
.TP
\fB\-x\fR
(0 arg) :    keep truncated bubbles, that have no successors on the 2 paths at the same position
.TP
\fB\-P\fR
(1 arg) :    maximal number of polymorphism per bubble  [default '1']
.TP
\fB\-D\fR
(1 arg) :    maximal size of a predicted indel  [default '0']
.TP
\fB\-dont_output_first_coverage\fR (0 arg) :
Don't output the first coverage threshold. Use this option whent the reference file is used for finding the variants
.TP
\fB\-in\fR
(1 arg) :    input file (likely a hdf5 file)
.TP
\fB\-coverage_file\fR
(1 arg) :    File (.h5) generated by kissnp2, containing the coverage threshold per read set  [default '_removemeplease']
.TP
\fB\-out\fR
(1 arg) :    output name
.TP
\fB\-T\fR
(0 arg) :    extend found and stop at large polymorphism (extension=contigs) SNPs. Uncompatible with \fB\-t\fR
.TP
\fB\-t\fR
(0 arg) :    extend found and stop at first polymorphism (strict extension=unitigs) SNPs. Uncompatible with \fB\-T\fR
.TP
\fB\-max_symmetrical_crossroads\fR (1 arg) :
In b2 mode only: maximal number of symmetrical croasroads traversed while trying to close a bubble. Default: no limit  [default '\-1']
.TP
\fB\-b\fR
(1 arg) :    branching mode
.IP
0: forbid SNPs for which any of the two paths is branching (high precision, low recall)
1: forbid SNPs for which the two paths are branching (e.g. the two paths can be created either with a 'A' or a 'C' at the same position (default value)
2: No limitation on branching (low precision, high recall)  [default '1']
.TP
\fB\-max_ambigous_indel\fR
(1 arg) :    Maximal size of ambiguity of INDELs. INDELS whose ambiguity is higher than this value are not output  [default '20']
.TP
\fB\-l\fR
(0 arg) :    conserve low complexity SNPs
.TP
\fB\-nb\-cores\fR
(1 arg) :    number of cores  [default '0']
.TP
\fB\-verbose\fR
(1 arg) :    verbosity level  [default '1']
.TP
\fB\-version\fR
(0 arg) :    version
.TP
\fB\-help\fR
(0 arg) :    help
.TP
\fB\-bfs\-max\-depth\fR
(1 arg) :    maximum depth for BFS  [default '200']
.TP
\fB\-bfs\-max\-breadth\fR
(1 arg) :    maximum breadth for BFS  [default '20']
.SH AUTHOR
This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.