Summary: Choose the scan step size Argument: < 'distance' or 'step' > < number >
If 'increment distance 2.0' is entered, the 'scan' command will calculate LODscores and NPL statistics every 2.0 cM throughout the genetic map selected (regardless of the position of markers in that map) as follows (in this example the off end distance is set to 6.0 cM):
-6.0 (6 cM before the first marker), -4.0, -2.0, 0.0 (the position of the first marker), 2.0, 4.0, ...etc...until 6.0 cM after the last locus.
If 'increment step 5' is selected, the scan command will calculate scores at 5 equally spaced positions between each marker. For example, with a three-locus map with 10 and 15 cM intervals and 'off-end' set to 5.0 cM, maps will be computed at the following positions:
-5.0, -4.0, -3.0, -2.0, -1.0 (equally spaced in the 5cM before the first marker) 0.0, 2.0, 4.0, 6.0, 8.0 (equally spaced in the 10 cM interval) 10.0, 13.0, 16.0, 19.0, 22.0 (equally spaced in the 15 cM interval) 25.0, 26.0, 27.0, 28.0, 29.0, 30.0 (equally spaced in the 5cM after the map)
The default value of 'increment' is 'step 5'. Calling 'increment' with no arguments causes GENEHUNTER to report the current value.
Note that the first ('distance') method is not guaranteed to hit every marker position and should be considered inferior to the second ('step') method, which will compute a map at every marker position.