wgsim - Man Page
Whole-genome sequencing read simulator
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