.TH WGSIM "1" "December 2015" "wgsim 1.2" "User Commands"
.SH NAME
wgsim \- short read simulator
.SH SYNOPSIS
.B wgsim
[\fI\,options\/\fR] \fI\,<in.ref.fa> <out.read1.fq> <out.read2.fq>\/\fR
.SH OPTIONS
.TP
\fB\-e\fR FLOAT
base error rate [0.020]
.TP
\fB\-d\fR INT
outer distance between the two ends [500]
.TP
\fB\-s\fR INT
standard deviation [50]
.TP
\fB\-N\fR INT
number of read pairs [1000000]
.TP
\fB\-1\fR INT
length of the first read [70]
.TP
\fB\-2\fR INT
length of the second read [70]
.TP
\fB\-r\fR FLOAT
rate of mutations [0.0010]
.TP
\fB\-R\fR FLOAT
fraction of indels [0.15]
.TP
\fB\-X\fR FLOAT
probability an indel is extended [0.30]
.TP
\fB\-S\fR INT
seed for random generator [\-1]
.TP
\fB\-h\fR
haplotype mode
.SH AUTHOR
The software was written by Heng Li <lh3@sanger.ac.uk>
.P
This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.