Overview

There are five subcommands in sstar:

• score
• quantile
• threshold
• matchrate
• tract

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

sstar subcommand -h

For example:

sstar score -h

Note: sstar score assumes variants are bi-allelic in the combined reference and target populations used for scoring. Source populations are used for downstream annotation and match-rate calculation, and should not determine which variants are retained for S* scoring. Please check your data carefully before using sstar. 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. sstar assumes individuals are diploid.

By default, sstar score reports one row per target individual using genotype dosages and sets hap_index to NA. With --phased, sstar score reports one row per target haplotype and uses hap_index to identify the haplotype. Downstream commands that consume score files should be run in the same mode as the score file when a --phased option is available.