mason_materializer - VCF Materialization
mason_materializer [OPTIONS] -ir IN.fa
-iv IN.vcf -o OUT.fa
Apply variants from IN.vcf to IN.fa and write the
results to out.fa.
- -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.
- -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-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.
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.