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

Info

18 July 2018 samtools-1.9 Bioinformatics tools