jpayne@68: .TH wgsim 1 "21 June 2017" "samtools-1.5" "Bioinformatics tools"
jpayne@68: .SH NAME
jpayne@68: wgsim \- Whole-genome sequencing read simulator
jpayne@68: .SH SYNOPSIS
jpayne@68: .B wgsim
jpayne@68: [\fI\,options\/\fR] \fI\,<in.ref.fa> <out.read1.fq> <out.read2.fq>\/\fR
jpayne@68: .PP
jpayne@68: <in.ref.fa> must be a fasta file containing a reference genome.
jpayne@68: .PP
jpayne@68: <out.read1.fq> and <out.read2.fq> are the first and second read output files.
jpayne@68: .SH OPTIONS
jpayne@68: .TP
jpayne@68: \fB\-e\fR FLOAT
jpayne@68: base error rate [0.000]
jpayne@68: .TP
jpayne@68: \fB\-d\fR INT
jpayne@68: outer distance between the two ends [500]
jpayne@68: .TP
jpayne@68: \fB\-s\fR INT
jpayne@68: standard deviation [50]
jpayne@68: .TP
jpayne@68: \fB\-N\fR INT
jpayne@68: number of read pairs [1000000]
jpayne@68: .TP
jpayne@68: \fB\-1\fR INT
jpayne@68: length of the first read [70]
jpayne@68: .TP
jpayne@68: \fB\-2\fR INT
jpayne@68: length of the second read [70]
jpayne@68: .TP
jpayne@68: \fB\-r\fR FLOAT
jpayne@68: rate of mutations [0.0010]
jpayne@68: .TP
jpayne@68: \fB\-R\fR FLOAT
jpayne@68: fraction of indels [0.15]
jpayne@68: .TP
jpayne@68: \fB\-X\fR FLOAT
jpayne@68: probability an indel is extended [0.30]
jpayne@68: .TP
jpayne@68: \fB\-S\fR INT
jpayne@68: seed for random generator [\-1]
jpayne@68: .TP
jpayne@68: \fB\-A\fR FLOAT
jpayne@68: discard if the fraction of ambiguous bases higher than FLOAT [0.05]
jpayne@68: .TP
jpayne@68: \fB\-h\fR
jpayne@68: haplotype mode
jpayne@68: .TP
jpayne@68: Parameter defaults are given in square brackets.
jpayne@68: .SH AUTHOR
jpayne@68: Copyright 2008 Genome Research Limited.
jpayne@68: .br
jpayne@68: Copyright 2011 Heng Li.
jpayne@68: .TP
jpayne@68: wgsim is part of samtools, https://github.com/samtools/samtools