This folder contains two source code used in Sidorenko et al. (2023) (1) predLink (2) 01_sim-sib-array.R (3) sibREML_v0.1.1.R (4) Summarised_genetic_map.txt (1) predLink predLink is a C++-based program that predicts linkage signals from association results Input: - an IBD file (--ibd): specifies for each position (in cM) what is the IBD probability. IBD probability output from Merlin - a step size (--step): Specifies step between markers to make prediction. Default is 1 (minimum is 1 cM). - a genotype file (--bfile): binary PLINK format for genotypes - a GWAS summary statistics file (--sumstat) - a chromosome number (--chr) - an output prefix (--out) ==> predLink can be compiled by typing: make ==> Help can be accessed by typing: ./predLink --help (2) 01_sim-sib-array.R This R script simulates genotypes of siblings from a set of haplotypes (from 962 trios in the UK Biobank) and recombination map. Input data are Maps: a folder containing 22 maps for each autosome (maps were downloaded from bcfTool website) Haplotypes: a folder containg 22 .RData file (one for each autsome). Each RData file is matrix of phased haplotypes map file: a PLINK map file bim file: a PLINK bim file Output - PLINK format genotypes for sibling pairs - RData objects containing the coordinates (chromosome, start, stop) and status of all IBD segments (3) sibREML_v0.1.1.R This R script implements a REstricted Maximum Likelihood (REML) estimation of genetic variance for independent families. The Average-Information algorithm implemented in this R script was previously described in Yang et al. AJHG (2011). (4) Summarised_genetic_map.txt This files contains 6388 (+1 header) rows and 5 columns sumamrising the genetic and physical coordinates of loci used in linkage analyses. An overview is shown below... CHR cM_Start cM_End Mb_Start Mb_End 1 0 0.5 0.010583 1.100217 1 0.5 1 1.100319 1.184244 1 1 1.5 1.185008 1.977507 1 1.5 2 1.977537 2.255633