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
--file-suffix	TEXT File suffix for output files
--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: