Subcommand: simulate

Create a file with simulated random frequency data.

Usage: grenedalf simulate [options]

Options

Settings
--format	TEXT:{pileup,sync}=pileup Select the output file format, either (m)pileup, or PoPollation2 sync.
--random-seed	UINT=0 Set the random seed for generating values, which allows reproducible results. If not provided, the system clock is used to obtain a random seed.
Samples
--coverages	Required. TEXT Coverages of the samples to simulate, as a comma- or tab-separated list. The coverage of each sample is used at the total count per position to randomly distribute across nucleotides. Per sample, the list can either contain a single number, which will be used as the coverage for that sample at each position, or it can be two numbers separated by a slash, which will be used as min/max to generate random coverage at each position. The length of this list is also used to determine the number of samples to simulate.
Genome
--chromosome	TEXT=A Name of the chromosome. This is simply used as the first column in the output file. At the moment, only one chromosome is supported.
--mutation-rate	FLOAT:(FLOAT in [0 - 1]) AND (POSITIVE)=1e-08 Excludes: --mutation-count Mutation rate to simulate. This rate times the --length is used as the number of mutations to generate in total (which can alternatively be directly provided via --mutation-count).
--mutation-count	UINT=0 Excludes: --mutation-rate Number of mutations to simulate in total across the chromosome, spread across the --length.
--length	Required. UINT=0 Total length of the chromosome to simulate. Mutations are spread across this length.
--omit-invariant-positions	If set, only write the mutated positions in the output file. Note that these are not standard (m)pileup or sync files any more; still this option might be useful.
Pileup
--with-quality-scores	If set, phred-scaled quality scores are written when simulating an (m)pileup file, using the --min-phred-score and --max-phred-score settings. Ignored otherwise.
--min-phred-score	UINT:UINT in [0 - 90]=10 Minimum phred score to use when simulating an (m)pileup file. Ignored otherwise.
--max-phred-score	UINT:UINT in [0 - 90]=40 Maximum phred score to use when simulating an (m)pileup file. Ignored otherwise.
Output
--out-dir	TEXT=. Directory to write files to
--file-prefix	TEXT File prefix for output files. Most grenedalf commands use the command name as the base name for file output. This option amends the base name, to distinguish runs with different data.
--file-suffix	TEXT File suffix for output files. Most grenedalf commands use the command name as the base name for file output. This option amends the base name, to distinguish runs with different data.
--compress	If set, compress the output files using gzip. Output file extensions are automatically extended by .gz.
Global Options
--allow-file-overwriting	Allow to overwrite existing output files instead of aborting the command.
--verbose	Produce more verbose output.
--threads	UINT Number of threads to use for calculations.
--log-file	TEXT Write all output to a log file, in addition to standard output to the terminal.

Citation

When using this method, please do not forget to cite

Lucas Czech, Moises Exposito-Alonso. Grenedalf: Genome Analyses of Differential Allele Frequencies. Manuscript in preparation, 2021. doi: