Input Parameters
All parameters can be viewed by typing the command without any parameter. The default choices are shown in [ ]. Parameters starting with '-' should be following an appropriate value. Parameters starting with '--' are switchers.
-f filename	input file name. 1) If genotypes are stored a single filie, they are named as 'filename.ped', 'filename.dat'. 2) For data separated into multiple files: they must be named as 'filename#.ped', 'filename#.dat' where # starts from 1 to N (N is specified in -c parameter).
-c	For data separated into multiple files. See the -f parameter.
-s	Definition of score for the similarity scores. We recommend using ibd or alleleibs. options are: ibd/alleleibs/rawibs/hweibs
-k	Power parameter in dissimilarity score, default =2 is recommended
-m	Number of markers to be use to compute the similarity scores. Usually 10,000-30,000 is sufficient. The more markers will often leads to more accurate matching, but needs more computation time.
-model	genetic model additive: additive model (x = 0, 1, 2, number of allele A) 2df: free model (x = (1, 0) if AA; (0, 1) if aa; (0, 0) if Aa)
-w	Window-size for selecting markers. number of marker times window-size cannot be greater than the total number of markers.
-nc	The total number of controls to be matched. If unspecified, all controls will be used.
-U	Maximum number of cases per matched set.
-Ut	Maximum number of controls per matched set. The values for -U and -Ut depends on the case:control ratio in the sample. Usually take the value between 2-5. A larger number may lead to a better matching by allowing more flexibility, but may lose a little of power when there is no stratification.
-o	association result output filename.
-os	output similarity scores between cases and controls or all pairs of individuals when --pairscore is in effect.
-om	output matching result.
-scoremarker	Output markers used for score calculation
--pairscore	If specified, the program will only compute the similarity score between each pair of individuals regardless of case and control labels. No matching or association analysis will be done. The output will be written to the file specified by the -os parameter. It can be used to get an idea about the stratification, e.g., it can be fed into a cluster analysis as similarity matrix.
--flexmatch	Perform matching at each locus for individuals with non-missing genotype. Recommended when missing rate is high but will take more time.
--matchonly	Only output matching results
--MHtest	Generalized Mantel-Haenszel test used with the additive model.
--random	Use random markers to compute similarity scores
-inputm	User specified matching input. Each line of the file contains 'FamID PersonID GroupID'. FamId and PersonID could be characters. GroupID should be intergers.
-inputScore	User provided score (similarity score) . Input score as a matrix, row=cases and col=controls. Please check "score.out" in the package for an example.