To run cntmono on your data, you first need to create the following files:
Individual file: List of all the parental samples of populations A and B that one would like to include in the analysis
Marker file: List of markers (same format as /ancestrymap/examples/snps)
Genotype file: Genotype data for the parental samples of populations A and B.
Aglistname: List of ethnicities that one would like to classify as population A (same format as: /ancestrymap/examples/aflist)
Eglistname: list of ethnicities that one would like to classify as population B (same format as: /ancestrymap/examples/eurlist)
Next make a copy of the /ancestrymap/examples/parmono
file, and specify the names of the various files in there.
Next type on the command line (go to the bin/ directory):
>> ./cntmono –p parmono
This will create a file in the same format as the marker file used by ANCESTRYMAP, for an example look at snp.dat in the examples/ directory.
Before using this file as the input marker file for ancestrymap, remove from it the blank lines, lines with comments and, the header line. This file should only contain details about the markers, else ancestrymap will give a fatal error.