KinInbcoefX Input Files May 25, 2009 The C++ program KinInbcoefX requires two input files: 1. pedigreefile - a file giving the pedigree and sex information for all individuals 2. listfile - a file listing individuals for whom X-chromosome inbreeding and kinship coefficients will be calculated. An X-chromosome inbreeding coefficient will be calculated for each individual, and an X-chromosome kinship coefficient will be calculated for each pair of distinct individuals who are in the same family. 1) Format for pedigreefile This input file should consist of a rectangular array of integers, with 5 columns. Each row contains information for one individual. The five columns are, in order: Family ID, Individual ID, Father's ID, Mother's ID, and Sex. Example: 1 1 0 0 2 1 4 0 0 1 1 2 4 1 1 1 3 4 1 2 2 2 1 5 1 2 8 1 5 2 2 9 1 5 2 2 5 0 0 2 2 1 0 0 1 (1) (2) (3) (4) (5) (1) Family ID (2) Individual ID (3) Father's ID (0 if the individual is a founder) (4) Mother's ID (0 if the individual is a founder) (5) Sex (1 = male, any other integer = female) Family ID's must be consecutive integers from 1 to F, without gaps, with members of the same family listed in consecutive rows, and with family 1 listed first, family 2 second, ..., and family F last. There is a limit MAXFAM to the number of families allowed. KinInbcoefX's source code has MAXFAM set to 100. To change this limit, change the value of MAXFAM in the source code and re-compile the program. Individual ID is a positive integer. Individuals in different families can have the same ID number, but individuals in the same family must not have the same ID number. The ID numbers need not be consecutive. There is a limit MAXIND on the number of individuals in a family. KinInbcoefX's source code has MAXIND set to 1000. To change this limit, change the value of MAXIND in the source code and re-compile the program. If the individual is not a founder, then Father's ID and Mother's ID are both positive integers. If the individual is a founder, then both Father's ID and Mother's ID should be set to 0. Sex is an integer that is 1 for male and any other integer for female. No blank spaces should follow the last row of data. The program will detect a particular kind of error in pedigreefile, namely a mismatch between a parent's status as a father or mother and the parent's sex. Consider, for example, the above pedigreefile example, with three such errors introduced. In family 1, individual 2 has individual 1 listed as a father, but individual 1 is listed as female. In family 1, individual 2 has individual 4 listed as a mother, but individual 4 is listed as male. In family 2, individual 9 has individual 1 listed as a mother, but individual 1 is listed as male. Example: 1 1 0 0 2 1 4 0 0 1 1 2 1 4 1 1 3 4 1 2 2 2 1 5 1 2 8 1 5 2 2 9 1 1 2 2 5 0 0 2 2 1 0 0 1 (1) (2) (3) (4) (5) (1) Family ID (2) Individual ID (3) Father's ID (0 if the individual is a founder) (4) Mother's ID (0 if the individual is a founder) (5) Sex (1 = male, any other integer = female) The program terminates after all such errors are detected. When such an error occurs, an error statement is printed to the screen and information about the error is printed to a file errorfile. For details on the printed error statement and errorfile, see Output.htm, which can be reached from the main KinInbcoefX page. 2) Format of listfile, which lists the individuals for whom X-chromosome kinship and inbreeding coefficients will be calculated. This input file should contain a rectangular array of integers with 2 columns. Each row contains information for one individual. This first column is Family ID and the second column is Individual ID. Example: 1 1 1 2 1 3 2 1 2 2 2 8 2 9 (1) (2) (1) Family ID (2) Individual ID A Family ID in the listfile should be the same as the corresponding Family ID in the pedigreefile. An individual ID in the listfile should be the same as the corresponding individual ID in the pedigreefile. No blank spaces should follow the last row of data.