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Man Pages


Manual Reference Pages  -  WGSIM (1)

NAME

wgsim - Whole-genome sequencing read simulator

CONTENTS

Synopsis
Options
Author

SYNOPSIS

wgsim [\,options\/] \,<in.ref.fa> <out.read1.fq> <out.read2.fq>\/

<in.ref.fa> must be a fasta file containing a reference genome.

<out.read1.fq> and <out.read2.fq> are the first and second read output files.

OPTIONS

-e FLOAT base error rate [0.000]
-d INT outer distance between the two ends [500]
-s INT standard deviation [50]
-N INT number of read pairs [1000000]
-1 INT length of the first read [70]
-2 INT length of the second read [70]
-r FLOAT rate of mutations [0.0010]
-R FLOAT fraction of indels [0.15]
-X FLOAT probability an indel is extended [0.30]
-S INT seed for random generator [-1]
-A FLOAT discard if the fraction of ambiguous bases higher than FLOAT [0.05]
-h haplotype mode
Parameter defaults are given in square brackets.
 

AUTHOR

Copyright 2008 Genome Research Limited.
Copyright 2011 Heng Li.
wgsim is part of samtools, https://github.com/samtools/samtools
 
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samtools-1.3 WGSIM (1) 15 December 2015

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