Kinship and Inbreeding coefficients computation in general pedigrees. Copyright(C) 2003 Catherine Bourgain Homepage: http://galton.uchicago.edu/~mcpeek/software/KinInbcoef/index.html Release 1.0. December 1,2003 =========================================================== License This program is a free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY of FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with this program (see file gpl.txt); if not, write to the Free Software Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. To contact the author: Catherine Bourgain INSERM U535 Bat.Leriche Hopital Paul Brousse BP 1000 94817 Villejuif Cedex France Tel : +33 1 45 59 53 85 Fax : +33 1 45 59 53 31 bourgain@vjf.inserm.fr =========================================================== This program computes inbreeding and kinship coefficients for general pedigrees using the algorithm proposed by KARIGL (1981,Ann. Hum Genet 45:299-305) 1. Input files Two input files are required : - a file with the pedigree information ('pedfile') Format is : 1 line per individual in the pedigree with 4 columns : 1 1 7 6 1 2 7 6 1 3 7 6 1 7 0 0 1 6 0 0 2 1 8 9 2 2 8 9 2 8 0 0 2 9 5 6 2 5 0 0 2 6 0 0 (1) (2) (3) (4) (1) family ID (2) individual ID (3) father's ID (0=unknown) (4) mother's ID (0=unknown) 0 should be used when parent are unavailable. Families should be numbered with following numbers from 1 to F, without gaps. There is a limit in the number of families to be analyzed at the same time (MAXFAM, currently set to 100). To increase this limit, just change the values of MAXFAM in the KinInbcoef.c source file and recompile the program. - a file with the list of the individuals for whom computation of the coefficients is required ('listfile') Format is : 1 line per individual with 2 columns : 1 1 1 2 1 3 2 1 2 2 2 8 2 9 (1) (2) (1) family ID (2) individual ID There is a limit in the total number of individuals in each family for whom coefficients are computed(MAXIND, currently set to 1000). To increase this limit, just change the values of MAXIND in the KinInbcoef.c source file and recompile the program. 2. Output file There is a single output file ('outputfile'). For each individual i listed in the listfile, the outputfile gives his inbreeding coefficient (hi) and his kinship coefficients with all the other members of his family which are also listed in the listfile. Format is : 1 1 1 0.0 1 1 2 0.25 1 1 3 0.25 1 2 2 0.0 1 2 3 0.25 1 3 3 0.0 2 1 1 0 2 1 2 0.25 2 1 8 0.25 2 1 9 0.25 . . . . . . . . (1) (2) (3) (4) (1) family ID (2) individual 1 ID (3) individual 2 ID (4) the inbreeding coefficient if ID1=ID2 the kinship coefficient otherwise NB : the outputfile has the exact format required for the kinship coefficient file needed to run the CC-QLS test 3. Usage Three arguments should be entered in the command line : name of the pedigreefile, name of the listfile and name of the outputfile : ./KinInbcoef pedigreefile listfile outputfile 4. Compilation A C++ compiler should be used to compile the program. When using the g++ compiler, just type : g++ KinInbcoef.c -o KinInbcoef 5. Example A 'pedtest' and a 'listtest' files are provided. Corresponding output file is also provided : 'outtest'. Try ./KinInbcoef pedtest listtest out and compare the results in the 'out' file with the results in the 'outtest' file