Command-Line Parameters of snp_detect Program
| Option name | Data type | Permitted range | Default value | Description |
| -k | integer | >0 | 7 | k-tuple length |
| -d | integer | >0 | 10 | Upper length limit for short gaps. |
| -b | integer | ≥0 | 2 | Number of base positions by which long gaps are automatically extended |
| -c | integer | >0 | 2 | Count multiplier for chromosomal sequences |
| -u | integer | >0 | 2 | Count multiplier for RNA sequences |
| -n | integer | >1 | 2 | Minimal count of ak-tuple allele required by SNP test |
| -f | real | 0–0.5 | 0.1 | Minimal fraction of ak-tuple allele required by SNP test |
| -s | integer | >1 | 10 | Minimal number of nonpolymorphic positions required between SNPs to be considered parts of different SNP regions |