---
name: "wgsim"
section: "1"
platform: "linux"
package: "samtools"
version: "1.21-1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/wgsim"
---

# wgsim(1)

short read simulator

## NAME

wgsim - short read simulator

## SYNOPSIS

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

## OPTIONS

- **-e** FLOAT

  base error rate \[0.020\]

- **-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 \[-1\]

- **-h**

  haplotype mode

## AUTHOR

The software was written by Heng Li \<lh3@sanger.ac.uk\>

This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.