mason_materializer - VCF Materialization

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

       mason_materializer - VCF Materialization

-h, --help
              Display the help message.

       --version
              Display version information.

       -q, --quiet
              Low verbosity.

       -v, --verbose
              Higher verbosity.

       -vv, --very-verbose
              Highest verbosity.

       --seedINTEGER
              Seed for random number generation. Default: 0.

       --meth-seedINTEGER
              Seed for methylation simulation random number generation. Default: 0.

       -o, --outOUTPUT_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-breakpointsOUTPUT_FILE
              TSV file to write breakpoints in variants to. Valid filetypes are: .txt and .tsv.

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

       --meth-fasta-inINPUT_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-outOUTPUT_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.

   ApplyVCFVariantstoReference:-ir, --input-referenceINPUT_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-vcfINPUT_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.

   MethylationLevelSimulation:--methylation-levels
              Enable methylation level simulation.

       --meth-cg-muDOUBLE
              Median of beta distribution for methylation level of CpG loci. In range [0..1]. Default: 0.6.

       --meth-cg-sigmaDOUBLE
              Standard  deviation  of  beta  distribution  for  methylation  level of CpG loci. In range [0..1].
              Default: 0.03.

       --meth-chg-muDOUBLE
              Median of beta distribution for methylation level of CHG loci. In range [0..1]. Default: 0.08.

       --meth-chg-sigmaDOUBLE
              Standard deviation of beta distribution for methylation  level  of  CHG  loci.  In  range  [0..1].
              Default: 0.008.

       --meth-chh-muDOUBLE
              Median of beta distribution for methylation level of CHH loci. In range [0..1]. Default: 0.05.

       --meth-chh-sigmaDOUBLE
              Standard  deviation  of  beta  distribution  for  methylation  level of CHH loci. In range [0..1].
              Default: 0.005.

mason_materializer [OPTIONS] -irIN.fa-ivIN.vcf-oOUT.fa

       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]                                                         MASON_MATERIALIZER(1)