README file for IBDN program:
IBDN is modified program of ERPA, which implements a method for assessing increased-allele sharing between all pairs of affected relatives within a pedigree. IBDN uses the UNKNOWN and MLINK programs of the LINKAGE package to perform risk calculations which provide information concerning the extent to which pairs of affected relatives share the same allele identical by descent at a particular genetic locus. It follows the principle of ERPA in using pedigree information to assess probabilities of particular marker genotypes when these cannot be unambiguously assigned, but is extended to include all pairs of relatives rather than only pairs of siblings.
(see APPENDIX if you want to know the details):
The following files are needed to run the IBDN(ERPA) part of Fastlinkage:
| ibdn.ped |
| exp.dat |
| obs.dat |
(1). DATA FILE:
ibdn.pre --- your data file.
ibdn.ped --- LINKAGE pedigree data file, generated by MAKEPED
program from file ibdn.pre.
(2). MARKER LOCI FILE:
exp.dat --- DON'T HAVE TO CHANGE.
(3). LOCUS DATA FILE:
obs.dat --- need to be modified.
To run the IBDN program, you simply type: ibdn The output file is: "ibdn.out". You can type the following command to clean the dummy files: make clean
The input file ibdn.pre for this is in the format: pedigree id individual id Father's id Mother's id gender affected? marker allele values for example, 1 1 0 0 1 2 1 2 1 2 0 0 2 2 1 3 1 3 0 0 1 2 1 2 1 4 0 0 2 2 1 3 1 5 1 2 1 2 0 0 1 6 3 4 2 2 0 0 1 7 5 6 1 2 1 3 1 8 5 6 2 2 1 1 1 9 5 6 1 2 2 3 The first line indicates that this is pedigree number 1, individual number 1, father id is zero (because individual 1 is a founder), mother id is zero (individual is a founder), gender is 1 (for male), individual is affected (1=unaffected, 2=affected, 0=unknown), and marker alleles are 1 and 3 (0 if missing). The last line indicates that this is (still) pedigree number 1, individual number 9, father id is 5, mother id is 6, gender is 1 (male), individual is affected, and marker alleles are 2 and 3. To prepare this file for IBDN, you must run the batch file MAKEPED.BAT with command-line arguments as follows: MAKEPED ibdn.pre ibdn.ped n . This is assuming that the input file is named ibdn.pre and the output file will be named ibdn.ped for input into IBDN. This process add some information to the pedigree file that is needed by mlink.
The file exp.dat specifies that there are two loci and that the second is a risk locus. A dummy marker locus with two alleles is first specified. Then follows the specification of the dummy affection locus, which is the same as for OBS.DAT.
The file obs.dat should be prepared as follows: 2 2 0 5 0 0.0 0.0 0 1 2 3 5 0.10 0.20 0.25 0.25 0.20 1 2 0.999999 0.000001 1 0 0 1 2 0 0 0.0 1 2.0 1.0 The first line of the file contains the numbers: 2 2 0 5 and the last contains the numbers: 1 2.0 1.0. There should be no blank lines before the first line or after the last line as described. Lines 5 and 6 may be edited to reflect the allele number and frequencies for the marker of interest. Line 5 above has the numbers: 3 5. The 3 is a code that indicates that this is a marker locus. The 5 indicates the number of different alleles that may be found at this locus. Line 6 is a list of allele probabilities corresponding to the number of alleles on line 5. So the allele coded 1 has a population frequency of 0.10, the allele coded 2 has a frequency of 0.20, and so on. ========== END OF README FILE =========== Written by L. Emily Yu; Nov., 1995.