table of contents
| 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 2.0.9 [tarball] |