1wgsim(1)                     Bioinformatics tools                     wgsim(1)
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NAME

6       wgsim - Whole-genome sequencing read simulator
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SYNOPSIS

9       wgsim [options] <in.ref.fa> <out.read1.fq> <out.read2.fq>
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11       <in.ref.fa> must be a fasta file containing a reference genome.
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13       <out.read1.fq>  and <out.read2.fq> are the first and second read output
14       files.
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OPTIONS

17       -e FLOAT
18              base error rate [0.000]
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20       -d INT outer distance between the two ends [500]
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22       -s INT standard deviation [50]
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24       -N INT number of read pairs [1000000]
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26       -1 INT length of the first read [70]
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28       -2 INT length of the second read [70]
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30       -r FLOAT
31              rate of mutations [0.0010]
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33       -R FLOAT
34              fraction of indels [0.15]
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36       -X FLOAT
37              probability an indel is extended [0.30]
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39       -S INT seed for random generator [-1]
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41       -A FLOAT
42              discard if the fraction of ambiguous  bases  higher  than  FLOAT
43              [0.05]
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45       -h     haplotype mode
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47       Parameter defaults are given in square brackets.
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AUTHOR

50       Copyright 2008 Genome Research Limited.
51       Copyright 2011 Heng Li.
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53       wgsim is part of samtools, https://github.com/samtools/samtools
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57samtools-1.9                     18 July 2018                         wgsim(1)