Genetic Architecture Reconciles Linkage and Association Studies of Complex Traits

This (zipped) folder contains 3 sub-folders:

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The "bin" folder contains fuctions and gentic maps needed for analyes
bin \
    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)
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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. 
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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
    README
The README is provided within the folder.
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