Input Part I (PREST) ============== 1. "pedigrees" file This file contains a set of pedigrees that are to be checked for pedigree errors. There are no limitations on the number of pedigrees or the number of individuals in a pedigree. Below is a sample pedigree file: 1 1 7 6 1 2 1 2 7 6 2 2 1 3 7 6 1 2 1 7 0 0 1 1 1 6 0 0 2 0 4 1 8 9 2 2 4 2 8 9 1 1 4 3 8 9 2 1 4 8 0 0 1 0 4 9 5 6 2 1 4 5 0 0 1 0 4 6 0 0 2 0 (1) (2) (3) (4) (5) (6) (1) family ID (2) individual ID (3) father's ID (0=unknown) (4) mother's ID (0=unknown) (5) sex (1=male, 2=female) (6) affection status (0=unknown, 1=unaffected, 2=affected) All codes should be non-negative integers. Column (6) is not used by PREST, so the entries for this column could just as well be all zeroes. 2. "chromfiles" file This file contains the names of marker and genotype data files. Each line contains the name of a marker file and a genotype data file for one chromosome. You may enter files for as many chromosomes as you wish, but DO NOT ENTER the sex chromosome (chromosome 23). Below is a sample. chr05.idx chr05.ped chr07.idx chr07.ped chr08.idx chr08.ped chr11.idx chr11.ped The format of the marker files is similar to that used by GENEHUNTER. Below is a sample marker file, named "chr05.idx" 4 << no. of loci 3 7 # D05S1685 0.011 0.003 0.517 0.285 0.006 0.159 0.019 << allele frequencies 3 9 # D05S689 0.012 0.037 0.076 0.151 0.311 0.252 0.124 0.034 0.003 3 6 # D05S685 0.014 0.005 0.101 0.297 0.131 0.452 3 7 # D05S445 0.007 0.119 0.038 0.163 0.541 0.112 0.020 0.125 0.051 0.221 << recombination fraction values All comments are optional and are ignored by the program. The first line contains the number of markers typed on that chromosome. This is followed by two lines for each marker. The first line for each marker contains the number "3" (obligatory, as in GENEHUNTER) followed by the number of alleles. The second line contains the allele frequencies, which must sum to 1. At the end of the file there is an additional line that has the marker spacings which are in recombination fraction (not in Morgans or centi-Morgans). Note that if there are n markers, there are only n-1 marker spacings. The format of the genotype data files is also similar to that used by GENEHUNTER. Below is a sample genotype data file, named "chr05.ped" 1 1 7 6 1 2 5 5 4 4 3 4 2 5 1 2 7 6 2 2 5 5 0 0 0 0 5 6 1 3 7 6 1 2 5 5 0 0 3 3 2 5 1 7 0 0 1 1 0 0 0 0 3 3 5 5 1 6 0 0 2 0 5 7 0 0 0 0 2 6 4 1 8 9 2 2 5 7 4 5 0 0 7 8 4 2 8 9 1 1 5 7 0 0 6 6 5 7 4 3 8 9 2 1 5 5 0 0 6 6 7 8 4 8 0 0 1 0 5 5 0 0 3 6 7 7 4 9 5 6 2 1 5 7 0 0 0 0 5 8 4 5 0 0 1 0 0 0 0 0 0 0 0 0 4 6 0 0 2 0 0 0 0 0 0 0 0 0 (1) (2) (3) (4) (5) (6) (g----------------) (1)-(6) as in the pedigree file (g) marker genotype data (0=unknown) Part II (ALTERTEST) ================== 1. "altertest_input" file This file contains a list of problematic relative pairs along with their user-specified null hypothesis that may be different from what the pedigree says. There are no limitations on the number of pairs. Each pair can be listed with more than one suspected relationship, but each relationship has its own line. Below is a sample input file: 4 1 3 2 4 1 3 6 4 2 5 7 4 5 8 5 (1) (2) (3) (4) (1) family ID (2) individual 1 ID (3) individual 2 ID (4) relationship to be used as the null hypothesis for the pair ( 1 = full-sib, 2 = half-sib, 3 = grandparent-grandchild, 4 = avuncular, 5 = first-cousin, 6 = unrelated, 7 = half-avuncular, 8 = half-first-cousin, 9 = half-sib-plus-first-cousin. 10 = parent-offspring, 11 = MZ twins ) (A pair is called half-sib-plus- first-cousin if they have the same mother and different fathers who are brothers, or the same father and different mothers who are sisters.) All codes should be non-negative integers. The last column is crucial. It is the user-specified null hypothesis, to be used in the calculation of the EIBD, AIBS, IBS and MLLR test statistics and in the simulation of the genotype data for the pair to assess significance. In the current implementation of ALTERTEST, only the 11 null relationship types listed above are allowed. 2. "chromfiles" file This file, and all the marker files and genotype data files whose names appear within it, are EXACTLY the same as in Part I (PREST).