- Description: - Determines if the linkage dis-equilibrium decay based on the r2 metric for each generation across the genome and surrounding QTL is calculated each generation.
- Option: yes or no.
- Usage: 'OUTPUT_LD: no'.
- Type: Optional. Default is no

- Description: - Determines whether genotypes are saved and at what generation to begin saving them.
- Options: - No or yes and if yes provide the generation at which to start exporting genotypes. Generation 0 is founder population.
- Usage: 'GENOTYPES: yes 0'.
- Type: Optional. Default is yes and starting at generation 0.

- Description: - Calculates the proportion of the genome in a ROH for each individual. Also the frequency of a SNP being in a ROH and the length of ROH the SNP is contained in is calculated across the genome for a specified generation number.
- Options:
- Usage: 'GENOME_ROH: 5 5 10 15'.
- Type: Optional.

- Description: - Calculates the additive (∑2pq[a + d(q − p)]²) and dominance (∑(2pqd)²) variance within 1Mb non-overlapping windows for each generation.
- Option: yes or no.
- Usage: 'WINDOWQTLVAR: no'.
- Type: Optional. Default is no

- Description: - For each generation selection has occurred, the estimated breeding value (EBV) along with their associated true breeding value (TBV) are outputted to a file for the parents and selection candidates. The output can be used to generate the accuracy and bias of EBV across generations.
- Option: yes or no.
- Usage: 'TRAINREFER_STATS: no'.
- Type: Optional. Default is no