DOI: 10.5281/zenodo.10416893
title: Genetic Architecture Reconciles Linkage and Association Studies of Complex Traits

description: 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.#**********************************************************************************************************