---
name: "mason_methylation"
section: "1"
platform: "linux"
package: "seqan-apps"
version: "2.4.0+dfsg-16"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/mason_methylation"
---

# mason\_methylation(1)

Methylation Level Simulation

## NAME

mason\_methylation - Methylation Level Simulation

## SYNOPSIS

**mason\_methylation** \[OPTIONS\] **-i** *IN.fa* **-o** *OUT.fa*

## DESCRIPTION

Simulate methylation levels for *IN.fa* and write them to *OUT.fa*.

## OPTIONS

- **-h**, **--help**

  Display the help message.

- **--version**

  Display version information.

- **-q**, **--quiet**

  Low verbosity.

- **-v**, **--verbose**

  Higher verbosity.

- **-vv**, **--very-verbose**

  Highest verbosity.

- **--seed** *INTEGER*

  Seed for RNG. Default: *0*.

- **-i**, **--in** *INPUT\_FILE*

  Input FASTA file with genome. Valid filetypes are: *.sam\[.\*\]*, *.raw\[.\*\]*, *.gbk\[.\*\]*, *.frn\[.\*\]*, *.fq\[.\*\]*, *.fna\[.\*\]*, *.ffn\[.\*\]*, *.fastq\[.\*\]*, *.fasta\[.\*\]*, *.faa\[.\*\]*, *.fa\[.\*\]*, *.embl\[.\*\]*, and *.bam*, where \* is any of the following extensions: *gz*, *bz2*, and *bgzf* for transparent (de)compression.

- **-o**, **--out** *INPUT\_FILE*

  Input FASTA file with genome. Valid filetypes are: *.sam\[.\*\]*, *.raw\[.\*\]*, *.frn\[.\*\]*, *.fq\[.\*\]*, *.fna\[.\*\]*, *.ffn\[.\*\]*, *.fastq\[.\*\]*, *.fasta\[.\*\]*, *.faa\[.\*\]*, *.fa\[.\*\]*, and *.bam*, where \* is any of the following extensions: *gz*, *bz2*, and *bgzf* for transparent (de)compression.

### Methylation Level Simulation:

- **--methylation-levels**

  Enable methylation level simulation.

- **--meth-cg-mu** *DOUBLE*

  Median of beta distribution for methylation level of CpG loci. In range \[0..1\]. Default: *0.6*.

- **--meth-cg-sigma** *DOUBLE*

  Standard deviation of beta distribution for methylation level of CpG loci. In range \[0..1\]. Default: *0.03*.

- **--meth-chg-mu** *DOUBLE*

  Median of beta distribution for methylation level of CHG loci. In range \[0..1\]. Default: *0.08*.

- **--meth-chg-sigma** *DOUBLE*

  Standard deviation of beta distribution for methylation level of CHG loci. In range \[0..1\]. Default: *0.008*.

- **--meth-chh-mu** *DOUBLE*

  Median of beta distribution for methylation level of CHH loci. In range \[0..1\]. Default: *0.05*.

- **--meth-chh-sigma** *DOUBLE*

  Standard deviation of beta distribution for methylation level of CHH loci. In range \[0..1\]. Default: *0.005*.