├── .gitignore ├── 0.r_scripts ├── GWAS_demo.R ├── GWAS_demo.ipynb ├── filter_genotype_data.R ├── mean_imputation.R └── median_imputation.R ├── 1.preparatory_steps ├── 01_download_data.sh ├── 01_get_data[OLD].sh ├── 02_prep_data.sh ├── clean_folder.sh ├── install_from_bioconductor.r ├── install_from_cran.r ├── install_from_source.r ├── prep_dogpheno.R ├── prep_rice_data.R ├── prep_rice_data_pipeline.R └── rice_group.reference ├── 2.pre-processing ├── 01_data_handling_and_eda.sh ├── 02_filtering.sh ├── clean_folder.sh ├── eda.R ├── filtering.R ├── hwe.R ├── phenotypes.R └── phenotypes.Rmd ├── 3.imputation ├── 01_imputation.sh ├── 02_knni.sh ├── clean_folder.sh ├── g_matrix.Rmd ├── hamming.R ├── knni.R ├── knni_illustration.Rmd └── knni_tidymodels.R ├── 4.gwas ├── 01_gwas.sh ├── PCA_screeplots.R ├── clean_folder.sh ├── gwas_genabel.R ├── gwas_glm.R ├── gwas_glm_advanced.R ├── gwas_glm_permutationTest.R ├── gwas_rrblup.R ├── gwas_sommer.R ├── gwas_statgengwas.R ├── rice_imputed.raw └── styles.css ├── 5.power_and_significance ├── MultipleTestingCorrection.R └── StatisticalPower_exercise.R ├── 6.steps ├── 1.get_data.sh ├── 2.step_filtering.sh ├── 3.step_imputation.sh ├── 4.gwas.sh └── clean_folder.sh ├── 7.pipeline ├── .snakemake │ ├── log │ │ ├── 2019-09-06T140609.203763.snakemake.log │ │ ├── 2019-09-12T191339.761150.snakemake.log │ │ ├── 2019-09-12T191538.292534.snakemake.log │ │ ├── 2019-09-12T191719.217828.snakemake.log │ │ ├── 2019-09-12T193951.180109.snakemake.log │ │ ├── 2019-09-13T152619.482413.snakemake.log │ │ ├── 2019-09-13T152653.449619.snakemake.log │ │ ├── 2019-09-13T152722.700525.snakemake.log │ │ ├── 2019-09-13T152722.845179.snakemake.log │ │ ├── 2019-09-17T142402.057208.snakemake.log │ │ ├── 2019-09-17T142548.107849.snakemake.log │ │ ├── 2019-09-17T142813.823266.snakemake.log │ │ ├── 2019-09-17T142839.327527.snakemake.log │ │ ├── 2019-09-17T142859.855430.snakemake.log │ │ ├── 2019-09-17T143037.136537.snakemake.log │ │ ├── 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2019-11-01T205236.246119.snakemake.log │ │ ├── 2019-11-01T205605.849528.snakemake.log │ │ └── 2019-11-01T210104.109754.snakemake.log │ └── metadata │ │ ├── YnJhY2NvX2ltcHV0ZWQucmF3X3NwZWVkX0dXQVMucmVzdWx0cw== │ │ ├── c3RlcHMvYnJhY2NvX2ZpbHRlcmVkLm1hcA== │ │ ├── c3RlcHMvYnJhY2NvX2ZpbHRlcmVkLnBlZA== │ │ ├── c3RlcHMvYnJhY2NvX2ZpbHRlcmVkLnZjZg== │ │ ├── c3RlcHMvYnJhY2NvX2ltcHV0ZWQubWFw │ │ ├── c3RlcHMvYnJhY2NvX2ltcHV0ZWQucGVk │ │ ├── c3RlcHMvYnJhY2NvX2ltcHV0ZWQucmF3 │ │ ├── c3RlcHMvYnJhY2NvX2ltcHV0ZWQudmNmLmd6 │ │ ├── c3RlcHMvcGFydXNfZmlsdGVyZWQubWFw │ │ ├── c3RlcHMvcGFydXNfZmlsdGVyZWQucGVk │ │ ├── c3RlcHMvcGFydXNfZmlsdGVyZWQudmNm │ │ ├── c3RlcHMvcGFydXNfaW1wdXRlZC52Y2YuZ3o= │ │ ├── c3RlcHMvcGFydXNfaW1wdXRlZC5tYXA= │ │ ├── c3RlcHMvcGFydXNfaW1wdXRlZC5wZWQ= │ │ ├── c3RlcHMvcGFydXNfaW1wdXRlZC5yYXc= │ │ ├── c3RlcHMvcmljZV9maWx0ZXJlZC52Y2Y= │ │ ├── c3RlcHMvcmljZV9maWx0ZXJlZC5tYXA= │ │ ├── c3RlcHMvcmljZV9maWx0ZXJlZC5wZWQ= │ │ ├── c3RlcHMvcmljZV9pbXB1dGVkLm1hcA== │ │ ├── c3RlcHMvcmljZV9pbXB1dGVkLnBlZA== │ │ ├── c3RlcHMvcmljZV9pbXB1dGVkLnJhdw== │ │ ├── c3RlcHMvcmljZV9pbXB1dGVkLnZjZi5neg== │ │ ├── cGFydXNfaW1wdXRlZC5yYXdfY2x1dGNoX0dXQVMucmVzdWx0cw== │ │ └── cmljZV9pbXB1dGVkLnJhd19QSF9HV0FTLnJlc3VsdHM= ├── Snakefile_GWAS.binary ├── Snakefile_GWAS.continuous ├── Snakefile_GWAS.continuous_knni ├── Snakefile_GWAS.parus ├── clean_folder.sh ├── example_pipeline │ ├── clean_folder.sh │ ├── command_lines.sh │ ├── example_snakefile │ ├── example_snakefile_2 │ ├── snp.map │ └── snp_reshuffled.map ├── snakefile_command_line_assignment.sh ├── snakefile_command_line_binary.sh ├── snakefile_command_line_continuous.sh └── snakefile_command_line_knni.sh ├── 8.collaborative_exercise ├── 1.get_data.sh ├── 2.steps_filtering.sh ├── 3.step_imputation.sh ├── 4.gwas.sh ├── README └── clean_folder.sh ├── LICENSE ├── README.md ├── _config.yml ├── basic_model ├── 1.Basis_of_linear_regression.R └── 2.exercise.Basis_of_logistic_regression.Rmd ├── cross_reference ├── Horn_Suid_Segregation_Tables.xlsx └── rice_group.reference ├── example_data ├── clean_folder.sh ├── dogs_imputed.raw_cleft_lip_GWAS.results ├── genotypes_demo.csv ├── genotypes_fruit_sim.csv ├── map_demo.csv ├── map_fruit_sim.csv ├── phenotypes_demo.csv ├── phenotypes_fruit_sim.csv ├── rice_phenotypes.txt ├── rice_reduced.map └── rice_reduced.raw ├── functional_analysis ├── Canis_familiaris.bkg_genes ├── README.md ├── dogs_imputed.raw_cleft_lip_GWAS.results ├── getGenesFromSNP.R ├── gwas_genesCfamiliaris.csv ├── gwas_snp.csv └── menu.PNG ├── literature ├── Pavan_2020-GwasRecommendations.pdf └── plantgenome2015.08.0073.pdf ├── model_extensions ├── 1.categorical_gwas.Rmd ├── 2.categorical_gwas_example.Rmd ├── 3.longitudinal_gwas.Rmd ├── gemma │ ├── 1.prep_for_gemma.sh │ ├── 2.make_kinship.sh │ ├── 3.run_gemma.sh │ ├── clean_folder.sh │ └── support_scripts │ │ ├── plot_results.R │ │ └── prep_covs_for_gemma.R ├── gwasurvivr_illustration.Rmd ├── material │ └── time_to_event.png ├── multi_locus │ ├── 1.prep_for_blink.sh │ ├── 2.multi_locus_gwas.R │ ├── clean_folder.sh │ └── prep_pheno_and_covs_for_blink.R ├── multi_trait │ ├── 1.prep_data.sh │ ├── 2.run_gwas.sh │ ├── clean_folder.sh │ ├── gwas_sommer_multitrait.R │ ├── gwas_sommer_multitrait.ipynb │ ├── gwas_sommer_multitrait_old.R │ └── prep_rice_data_multi.R └── regenie │ ├── 1.prep_for_step1.sh │ ├── 2.regenie_step1.sh │ ├── 3.regenie_step2.sh │ ├── clean_folder.sh │ ├── plot_results.R │ └── prep_covs.R ├── model_extensions_data ├── BreastTissue.xls ├── GenRiz44.txt ├── Race_clincial_trial_Spreadsheet_de-identified__noagegender_final.xlsx ├── sheep_phenotypes.txt ├── sheep_reduced.map └── sheep_reduced.raw ├── slides ├── 0_General_Introduction.pdf ├── 10.A bioinformatic pipeline for GWAS (1).pdf ├── 10.A bioinformatic pipeline for GWAS.pdf ├── 11.Exploring Functionality with FUMA & DAVID.pdf ├── 12.1 GWAS_model_extensions_genotype_codification.pdf ├── 12.3.GWAS_model_extensions_trait_type.pdf ├── 14.ROH-based 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