VCFY

It generates a VCF file with simulated random variants based on the given probability model.

Tools

vcfy

Usage: vcfy [OPTIONS] REFERENCE

  Generate VCF file with simulated variants in specified range [low, high)
  for the given region of the reference genome (in FASTA format). In case
  that the region is not specified the first region is used. If no range is
  provided, it is assumed that the variants are scattered throughout the
  region.

  For more information, consult with the README file.

Options:
  -o, --output FILENAME      Write to this file instead of standard output.
  -m, --mutation-rate FLOAT  Base mutation rate.  [required]
  -r, --region TEXT          Region ID (default=first region in the reference)
  -l, --low INTEGER          Range lower bound (default=first locus in the
                             region)
  -h, --high INTEGER         Range upper bound (default=last locus in the
                             region)
  --help                     Show this message and exit.

ksnper

Usage: ksnper [OPTIONS] [VCF]

  Report the number of SNPs in all k-mers. Specify the k and the VCF file,
  it reports number of SNPS occurred in each k-mer.

Options:
  -o, --output FILENAME           Write to this file instead of standard
                                  output.
  -r, --reference FILENAME        Reference genome FASTA file. It will be
                                  inferred from VCF header, if not specified.
  -k INTEGER                      The value of k.  [required]
  -c                              Set if the input VCF is compressed
  -d, --dialect [unix|excel-tab|excel]
                                  Use this CSV dialect.  [default: unix]
  --help                          Show this message and exit.