.TH wgsim 1 "21 June 2017" "samtools-1.5" "Bioinformatics tools"
.SH NAME
wgsim \- Whole-genome sequencing read simulator
.SH SYNOPSIS
.B wgsim
[\fI\,options\/\fR] \fI\,<in.ref.fa> <out.read1.fq> <out.read2.fq>\/\fR
.PP
<in.ref.fa> must be a fasta file containing a reference genome.
.PP
<out.read1.fq> and <out.read2.fq> are the first and second read output files.
.SH OPTIONS
.TP
\fB\-e\fR FLOAT
base error rate [0.000]
.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\-A\fR FLOAT
discard if the fraction of ambiguous bases higher than FLOAT [0.05]
.TP
\fB\-h\fR
haplotype mode
.TP
Parameter defaults are given in square brackets.
.SH AUTHOR
Copyright 2008 Genome Research Limited.
.br
Copyright 2011 Heng Li.
.TP
wgsim is part of samtools, https://github.com/samtools/samtools