Genetic Architecture Reconciles Linkage and Association Studies of Complex Traits

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