Overview

sstar2 assumes biallelic genotype data with derived alleles coded as 1 and supports both phased and unphased data.

There are four subcommands in sstar2:

• train
• infer
• match
• assign

To display help information for each subcommand, users can use:

sstar2 <subcommand> -h

For example:

sstar2 train -h

If you need further help, such as reporting a bug or suggesting a feature, please open an issue.

Note: In this manual, we define the population without introgressed fragments as the reference population, the population receiving introgressed fragments as the target population, and the population donating introgressed fragments as the source population.

The example commands assume that users have cloned the sstar GitHub repository and run the commands from the root directory of the repository:

git clone https://github.com/xin-huang/sstar
cd sstar