This (zipped) folder contains 3 sub-folders: #**********************************************************************************************************The "bin" folder contains fuctions and gentic maps needed for analyesbin \ predLink.R - function to predict linkage sibREML_v0.1.1.R - function to run SibREML sim-sib-array.R - script to simulate sib-pairs from parental haplotypes Summarised_genetic_map_bcf.txt - genetic map per 0.5-cM long segments, based on map from bcftools (BCFtools: https://samtools.github.io/bcftools/bcftools.html) Summarised_genetic_map_OMNI.txt - genetic map per 0.5-cM long segments, based on OMNI map (https://github.com/joepickrell/1000-genomes-genetic-maps/tree/master/interpolated_OMNI)#********************************************************************************************************** #**********************************************************************************************************The "SIM" folder contains the simulation pipeline (scripts 01-15) as well as IBD sharing and simulated phenotypes for Simulated sib-pairs.SIM \ 01_sim-sib-array.sh *pre-run* 02_bed_recode_bcf_map.sh *pre-run* 03_make_merlin.R *pre-run* 04_error_merlin.sh *pre-run* 05_merlin_IBD.sh *pre-run* 06_sample_causal_snps.R *pre-run* 07_simulate_pheno.sh *pre-run* 08_bhat_gwas.R *can be run using provided data* 09_Linkage_VH.R *can be run using provided data* 10_predLink.R *can be run using provided data* 11_phi_hat.R *can be run using provided data* 12_IBD_Mb.R *can be run using provided data* 13_IBD_cM_recombrate_stratified.R *can be run using provided data* 14_SibREML.R *can be run using provided data* 15_SibREML_stratified_Q4.R *can be run using provided data* causal_snps \ *provided causal SNPs* IBD_results \ *provided IBD-probabilities for 1000 simulated sib-pairs* Linkage_VH_results \ pheno \ *provided simulated phenotypes (h2=1) for 8 genetic architectures* Phi_hat_results.txt predicted \ README SibREML_results.txt SibREML_stratified_Q4.txt The data can be used to run Linkage analysis, predict linkage, estimate phi_hat, as well as estimate non-stratified and recombination rate stratified sib-heritability (h2_FS and c).The README is provided within the folder. #********************************************************************************************************** #**********************************************************************************************************The "HT_BMI" folder contains data and scripts to predict linkage and estimate phi_hat for height and BMI.HT_BMI \ 01_predLink_HT_BMI.R 02_phi_hat_HT_BMI.R gws_sumstats \ *provided summary GWAS summary statistics to predict linkage for height and BMI* Linkage_results \ *provided linkage meta-analysis results for height and BMI from this study* Phi_hat_results_HT_BMI.txt PREDLINK_bmi.txt PREDLINK_height.txt READMEThe README is provided within the folder.#**********************************************************************************************************