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grenedalf is a collection of commands for working with population genetic data.

Many commands in grenedalf are re-implementations of commands of the PoPoolation and PoPoolation2 tools. However, being written in C++, grenedalf is much faster and needs less memory.

General usage

• Setup
• Overview
• Input
• Filtering
• Windowing
• Output
• Example

Command Line Interface

grenedalf is used via its command line interface, with commands for each task. The commands have the general structure:

grenedalf <command> [options]

Use grenedalf --help to get an overview of all commands, and use grenedalf <command> --help for the list of options of each command. The pages below also list these options, along with additional information on each command.

Commands

Command	Description
cathedral-plot	Create a cathedral plot, using the pre-computated cathedral data.
citation	Print references to be cited when using grenedalf.
diversity	Compute pool-sequencing corrected diversity measures Theta Pi, Theta Watterson, and Tajima's D.
frequency	Create a table with per-sample and/or total base counts and/or frequencies at positions in the genome.
fst	Compute pool-sequencing corrected measures of FST.
fst-cathedral	Compute the data for an FST cathedral plot.
license	Show the license of grenedalf.
simulate	Create a file with simulated random frequency data.
sync	Create a sync file that lists per-sample base counts at each position in the genome.
version	Extended version information about grenedalf.