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MASON_MATERIALIZER(1) MASON_MATERIALIZER(1)

NAME

mason_materializer - VCF Materialization

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
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: .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.
--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: .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.
--meth-fasta-out OUTPUT_FILE
FASTA file with methylation levels of the output file. 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.

Apply VCF Variants to Reference:

-ir, --input-reference INPUT_FILE
Path to FASTA file to read the reference from. 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.
-iv, --input-vcf INPUT_FILE
Path to the VCF file with variants to apply. Valid filetype is: .vcf[.*], 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.

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.

mason_materializer 2.0.8 [tarball]