NAME¶

SYNOPSIS

mason_materializer [OPTIONS] -ir IN.fa -iv IN.vcf -o OUT.fa

DESCRIPTION

Apply variants from IN.vcf to IN.fa and write the results to out.fa.

OPTIONS

-h, --help

Display the help message.

--version-check BOOL

Turn this option off to disable version update notifications of the application. One of 1, ON, TRUE, T, YES, 0, OFF, FALSE, F, and NO. Default: 1.

--version

Display version information.

-q, --quiet

Low verbosity.

-v, --verbose

Higher verbosity.

-vv, --very-verbose

Highest verbosity.

--seed INTEGER

Seed for random number generation. Default: 0.

--meth-seed INTEGER

Seed for methylation simulation random number generation. Default: 0.

-o, --out OUTPUT_FILE

Output of materialized contigs. Valid filetypes are: .fasta and .fa.

--out-breakpoints OUTPUT_FILE

TSV file to write breakpoints in variants to. Valid filetypes are: .txt and .tsv.

--haplotype-name-sep STRING

String separating contig name from haplotype number. Default: /.

--meth-fasta-in INPUT_FILE

FASTA file with methylation levels of the input file. Valid filetypes are: .fasta and .fa.

--meth-fasta-out OUTPUT_FILE

FASTA file with methylation levels of the output file. Valid filetypes are: .fasta and .fa.

Apply VCF Variants to Reference:

-ir, --input-reference INPUT_FILE

Path to FASTA file to read the reference from. Valid filetypes are: .fasta and .fa.

-iv, --input-vcf INPUT_FILE

Path to the VCF file with variants to apply. Valid filetype is: .vcf.

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.

VCF VARIANT NOTES

If the option --input-vcf/-iv is given then the given VCF file is read and the variants are applied to the input reference file. If it is not given then the input reference file is taken verbatimly for simulating reads.

There are some restrictions on the VCF file and the application of the variants to the reference will fail if the VCF file is non-conforming. VCF files from the mason_variator program are guaranteed to be read.

Only the haplotypes of the first individual will be generated.

VERSION

Last update: mason_materializer version: 2.0.7 [tarball] SeqAn version: 2.3.1