---
name: "dwgsim"
section: "1"
platform: "linux"
package: "dwgsim"
version: "0.1.14-3"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/dwgsim"
---

# dwgsim(1)

a short read simulator

## NAME

dwgsim: - a short read simulator

## SYNOPSIS

**dwgsim** \[*options*\] *\<in.ref.fa\> \<out.prefix\>*

## DESCRIPTION

DWGSIM is a short read simulator which simulates reads from modern sequencing platforms.

## OPTIONS

- **-e** FLOAT

  per base/color/flow error rate of the first read \[from 0.020 to 0.020 by 0.000\]

- **-E** FLOAT

  per base/color/flow error rate of the second read \[from 0.020 to 0.020 by 0.000\]

- **-i**

  use the inner distance instead of the outer distance for pairs \[False\]

- **-d** INT

  outer distance between the two ends for pairs \[500\]

- **-s** INT

  standard deviation of the distance for pairs \[50.000\]

- **-N** INT

  number of read pairs (**-1** to disable) \[-1\]

- **-C** FLOAT

  mean coverage across available positions (**-1** to disable) \[100.00\]

- **-1** INT

  length of the first read \[70\]

- **-2** INT

  length of the second read \[70\]

- **-r** FLOAT

  rate of mutations \[0.0010\]

- **-F** FLOAT

  frequency of given mutation to simulate low fequency somatic mutations \[0.5000\] NB: freqeuncy F refers to the first strand of mutation, therefore mutations on the second strand occur with a frequency of 1-F

- **-R** FLOAT

  fraction of mutations that are indels \[0.10\]

- **-X** FLOAT

  probability an indel is extended \[0.30\]

- **-I** INT

  the minimum length indel \[1\]

- **-y** FLOAT

  probability of a random DNA read \[0.05\]

- **-n** INT

  maximum number of Ns allowed in a given read \[0\]

- **-c** INT

  generate reads for \[0\]: 0: Illumina 1: SOLiD 2: Ion Torrent

- **-S** INT

  generate reads \[0\]: 0: default (opposite strand for Illumina, same strand for SOLiD/Ion Torrent) 1: same strand (mate pair) 2: opposite strand (paired end)

- **-f** STRING

  the flow order for Ion Torrent data \[(null)\]

- **-B**

  use a per-base error rate for Ion Torrent data \[False\]

- **-H**

  haploid mode \[False\]

- **-z** INT

  random seed (**-1** uses the current time) \[-1\]

- **-M**

  generate a mutations file only \[False\]

- **-m** FILE

  the mutations txt file to re-create \[not using\]

- **-b** FILE

  the bed-like file set of candidate mutations \[(null)\]

- **-v** FILE

  the vcf file set of candidate mutations (use pl tag for strand) \[(null)\]

- **-x** FILE

  the bed of regions to cover \[not using\]

- **-P** STRING

  a read prefix to prepend to each read name \[not using\]

- **-q** STRING

  a fixed base quality to apply (single character) \[not using\]

- **-Q** FLOAT

  standard deviation of the base quality scores \[2.00\]

- **-s** INT

  standard deviation of the distance for pairs \[50.000\]

- **-h**

  print this message

Note: For SOLiD mate pair reads and BFAST, the first read is F3 and the second is R3. For SOLiD mate pair reads and BWA, the reads in the first file are R3 the reads annotated as the first read etc.

Note: The longest supported insertion is 4294967295.