├── .dockerignore ├── .gitattributes ├── .github ├── ISSUE_TEMPLATE │ ├── bug_report.md │ ├── documentation-issue.md │ └── feature_request.md ├── pull_request_template.md └── workflows │ ├── docker.yml │ ├── docker_build_gwas.yml │ ├── docker_build_hello.yml │ ├── docker_build_push_gwas.yml │ ├── docker_build_push_hello.yml │ ├── docker_build_push_python3.yml │ ├── docker_build_push_r.yml │ ├── docker_build_python3.yml │ ├── docker_build_r.yml │ ├── greetings.yml │ ├── python.yml │ └── stale.yml ├── .gitignore ├── .readthedocs.yml ├── CHANGELOG.md ├── CONTRIBUTING.md ├── INSTALL.md ├── LICENSE ├── README.md ├── RELEASES.md ├── citation.cff ├── containers ├── README.md └── pull_all_containers.py ├── docker ├── Makefile ├── README.md ├── dockerfiles │ ├── gwas │ │ └── Dockerfile │ ├── hello │ │ └── Dockerfile │ ├── python3 │ │ └── Dockerfile │ └── r │ │ └── Dockerfile └── scripts │ ├── R │ ├── bioconductor.R │ ├── cran.R │ ├── github.R │ └── source.R │ ├── apt_get_essential.sh │ ├── build_docker.sh │ ├── convert_docker_image_to_singularity.sh │ ├── install_bcftools.sh │ ├── install_beagle.sh │ ├── install_bedtools.sh │ ├── install_bgenix.sh │ ├── install_bolt.sh │ ├── install_duohmm.sh │ ├── install_eagle.sh │ ├── install_flashpca.sh │ ├── install_gcta.sh │ ├── install_gctb.sh │ ├── install_gwama.sh │ ├── install_htslib.sh │ ├── install_king.sh │ ├── install_ldak.sh │ ├── install_liftover.sh │ ├── install_metal.sh │ ├── install_miniforge.sh │ ├── install_minimac4.sh │ ├── install_plink.sh │ ├── install_plink2.sh │ ├── install_plink2_avx2.sh │ ├── install_prsice.sh │ ├── install_qctools.sh │ ├── install_regenie.sh │ ├── install_samtools.sh │ ├── install_shapeit4.sh │ ├── install_shapeit5.sh │ ├── install_shapeit5_static.sh │ ├── install_simu.sh │ ├── install_snptest.sh │ ├── install_switchError.sh │ ├── install_vcftools.sh │ ├── move_singularity_file.sh │ ├── patches │ ├── eagle.diff │ ├── shapeit4.makefile.diff │ ├── shapeit5.diff │ ├── switchError.diff │ └── xcftools.diff │ ├── python_convert.sh │ └── stub.sh ├── docs ├── README.md └── containers │ ├── README.md │ ├── gwas.md │ ├── hello.md │ ├── python3.md │ └── r.md ├── environment.yml ├── pytest.ini ├── reference ├── README.md ├── examples │ ├── boltlmm │ │ ├── Readme.md │ │ ├── example_3chr.LDSCORE.tab │ │ ├── example_3chr.lmm.pheno │ │ └── example_3chr.snplist │ ├── gctb_2.0_tutorial │ │ ├── .gitattributes │ │ ├── README │ │ ├── about.txt │ │ ├── data │ │ │ ├── .DS_Store │ │ │ ├── 1000G_eur_chr22.bed │ │ │ ├── 1000G_eur_chr22.bim │ │ │ ├── 1000G_eur_chr22.fam │ │ │ └── 1000G_eur_chr22.freq │ │ ├── gwas │ │ │ ├── plink_submit_combination.sh │ │ │ ├── sim_1.assoc.linear │ │ │ ├── sim_1.log │ │ │ ├── sim_10.assoc.linear │ │ │ ├── sim_10.log │ │ │ ├── sim_11.assoc.linear │ │ │ ├── sim_11.log │ │ │ ├── sim_12.assoc.linear │ │ │ ├── sim_12.log │ │ │ ├── sim_13.assoc.linear │ │ │ ├── sim_13.log │ │ │ ├── sim_14.assoc.linear │ │ │ ├── sim_14.log │ │ │ ├── sim_15.assoc.linear │ │ │ ├── sim_15.log │ │ │ ├── sim_16.assoc.linear │ │ │ ├── sim_16.log │ │ │ ├── sim_17.assoc.linear │ │ │ ├── sim_17.log │ │ │ ├── sim_18.assoc.linear │ │ │ ├── sim_18.log │ │ │ ├── sim_19.assoc.linear │ │ │ ├── sim_19.log │ │ │ ├── sim_2.assoc.linear │ │ │ ├── sim_2.log │ │ │ ├── sim_20.assoc.linear │ │ │ ├── sim_20.log │ │ │ ├── sim_3.assoc.linear │ │ │ ├── sim_3.log │ │ │ ├── sim_4.assoc.linear │ │ │ ├── sim_4.log │ │ │ ├── sim_5.assoc.linear │ │ │ ├── sim_5.log │ │ │ ├── sim_6.assoc.linear │ │ │ ├── sim_6.log │ │ │ ├── sim_7.assoc.linear │ │ │ ├── sim_7.log │ │ │ ├── sim_8.assoc.linear │ │ │ ├── sim_8.log │ │ │ ├── sim_9.assoc.linear │ │ │ └── sim_9.log │ │ ├── ldm │ │ │ ├── genetic_map │ │ │ │ └── chr22.OMNI.interpolated_genetic_map │ │ │ ├── makeldm_full.sh │ │ │ ├── makeldm_full_mcpu.sh │ │ │ ├── makeldm_shrunk.sh │ │ │ ├── makeldm_shrunk_mcpu.sh │ │ │ ├── makeldm_sparse.sh │ │ │ ├── merge_full_mcpu.sh │ │ │ ├── merge_shrunk_mcpu.sh │ │ │ ├── shrunk │ │ │ │ └── chr22 │ │ │ │ │ ├── 1000G_eur_chr22.ldm.shrunk.info │ │ │ │ │ ├── 1000G_eur_chr22.ldm.shrunk.log │ │ │ │ │ ├── 1000G_eur_chr22.ldm.sparse.bin │ │ │ │ │ ├── 1000G_eur_chr22.ldm.sparse.info │ │ │ │ │ ├── make_shrunk_sparse.sh │ │ │ │ │ └── makeldm.job │ │ │ ├── shrunk_mcpu │ │ │ │ └── chr22 │ │ │ │ │ ├── 1000G_eur_chr22.ldm.shrunk.info │ │ │ │ │ ├── 1000G_eur_chr22.log │ │ │ │ │ ├── 1000G_eur_chr22.mldmlist │ │ │ │ │ ├── 1000G_eur_chr22.snp1-5000.ldm.shrunk.info │ │ │ │ │ ├── 1000G_eur_chr22.snp1-5000.ldm.shrunk.log │ │ │ │ │ ├── 1000G_eur_chr22.snp10001-15000.ldm.shrunk.info │ │ │ │ │ ├── 1000G_eur_chr22.snp10001-15000.ldm.shrunk.log │ │ │ │ │ ├── 1000G_eur_chr22.snp15001-20000.ldm.shrunk.info │ │ │ │ │ ├── 1000G_eur_chr22.snp15001-20000.ldm.shrunk.log │ │ │ │ │ ├── 1000G_eur_chr22.snp5001-10000.ldm.shrunk.info │ │ │ │ │ ├── 1000G_eur_chr22.snp5001-10000.ldm.shrunk.log │ │ │ │ │ ├── makeldm.job │ │ │ │ │ ├── merge.job │ │ │ │ │ ├── merge.pbspro │ │ │ │ │ ├── merge_1.pbspro │ │ │ │ │ └── merge_2.pbspro │ │ │ └── sparse │ │ │ │ └── chr22 │ │ │ │ ├── 1000G_eur_chr22.ldm.sparse.bin │ │ │ │ ├── 1000G_eur_chr22.ldm.sparse.info │ │ │ │ ├── 1000G_eur_chr22.ldm.sparse.log │ │ │ │ └── makeldm.job │ │ ├── ma │ │ │ ├── ma_create.R │ │ │ ├── ma_create_submit.sh │ │ │ ├── sim_1.ma │ │ │ ├── sim_10.ma │ │ │ ├── sim_11.ma │ │ │ ├── sim_12.ma │ │ │ ├── sim_13.ma │ │ │ ├── sim_14.ma │ │ │ ├── sim_15.ma │ │ │ ├── sim_16.ma │ │ │ ├── sim_17.ma │ │ │ ├── sim_18.ma │ │ │ ├── sim_19.ma │ │ │ ├── sim_2.ma │ │ │ ├── sim_20.ma │ │ │ ├── sim_3.ma │ │ │ ├── sim_4.ma │ │ │ ├── sim_5.ma │ │ │ ├── sim_6.ma │ │ │ ├── sim_7.ma │ │ │ ├── sim_8.ma │ │ │ └── sim_9.ma │ │ ├── pheno │ │ │ ├── phenos_ga1.txt │ │ │ ├── snp_effects_ga1_sim_1.txt │ │ │ ├── snp_effects_ga1_sim_10.txt │ │ │ ├── snp_effects_ga1_sim_11.txt │ │ │ ├── snp_effects_ga1_sim_12.txt │ │ │ ├── snp_effects_ga1_sim_13.txt │ │ │ ├── snp_effects_ga1_sim_14.txt │ │ │ ├── snp_effects_ga1_sim_15.txt │ │ │ ├── snp_effects_ga1_sim_16.txt │ │ │ ├── snp_effects_ga1_sim_17.txt │ │ │ ├── snp_effects_ga1_sim_18.txt │ │ │ ├── snp_effects_ga1_sim_19.txt │ │ │ ├── snp_effects_ga1_sim_2.txt │ │ │ ├── snp_effects_ga1_sim_20.txt │ │ │ ├── snp_effects_ga1_sim_3.txt │ │ │ ├── snp_effects_ga1_sim_4.txt │ │ │ ├── snp_effects_ga1_sim_5.txt │ │ │ ├── snp_effects_ga1_sim_6.txt │ │ │ ├── snp_effects_ga1_sim_7.txt │ │ │ ├── snp_effects_ga1_sim_8.txt │ │ │ ├── snp_effects_ga1_sim_9.txt │ │ │ ├── variances_ga1_sim_1.txt │ │ │ ├── variances_ga1_sim_10.txt │ │ │ ├── variances_ga1_sim_11.txt │ │ │ ├── variances_ga1_sim_12.txt │ │ │ ├── variances_ga1_sim_13.txt │ │ │ ├── variances_ga1_sim_14.txt │ │ │ ├── variances_ga1_sim_15.txt │ │ │ ├── variances_ga1_sim_16.txt │ │ │ ├── variances_ga1_sim_17.txt │ │ │ ├── variances_ga1_sim_18.txt │ │ │ ├── variances_ga1_sim_19.txt │ │ │ ├── variances_ga1_sim_2.txt │ │ │ ├── variances_ga1_sim_20.txt │ │ │ ├── variances_ga1_sim_3.txt │ │ │ ├── variances_ga1_sim_4.txt │ │ │ ├── variances_ga1_sim_5.txt │ │ │ ├── variances_ga1_sim_6.txt │ │ │ ├── variances_ga1_sim_7.txt │ │ │ ├── variances_ga1_sim_8.txt │ │ │ └── variances_ga1_sim_9.txt │ │ ├── pheno_generation │ │ │ ├── 1000G_genos_scaled.Rdata │ │ │ ├── pheno_generate.R │ │ │ ├── pheno_generate_validation.R │ │ │ ├── read_plink_func.R │ │ │ └── ukb_eu_hm3_chr21_22_scaled.Rdata │ │ └── sbayesr │ │ │ ├── gctb_out_r_1000G_eur_shrunk │ │ │ ├── sim_1.covRes │ │ │ ├── sim_1.log │ │ │ ├── sim_1.mcmcsamples.CovEffects │ │ │ ├── sim_1.mcmcsamples.Par │ │ │ ├── sim_1.parRes │ │ │ ├── sim_1.snpRes │ │ │ ├── sim_10.covRes │ │ │ ├── sim_10.log │ │ │ ├── sim_10.mcmcsamples.CovEffects │ │ │ ├── sim_10.mcmcsamples.Par │ │ │ ├── sim_10.parRes │ │ │ ├── sim_10.snpRes │ │ │ ├── sim_11.covRes │ │ │ ├── sim_11.log │ │ │ ├── sim_11.mcmcsamples.CovEffects │ │ │ ├── sim_11.mcmcsamples.Par │ │ │ ├── sim_11.parRes │ │ │ ├── sim_11.snpRes │ │ │ ├── sim_12.covRes │ │ │ ├── sim_12.log │ │ │ ├── sim_12.mcmcsamples.CovEffects │ │ │ ├── sim_12.mcmcsamples.Par │ │ │ ├── sim_12.parRes │ │ │ ├── sim_12.snpRes │ │ │ ├── sim_13.covRes │ │ │ ├── sim_13.log │ │ │ ├── sim_13.mcmcsamples.CovEffects │ │ │ ├── sim_13.mcmcsamples.Par │ │ │ ├── sim_13.parRes │ │ │ ├── sim_13.snpRes │ │ │ ├── sim_14.covRes │ │ │ ├── sim_14.log │ │ │ ├── sim_14.mcmcsamples.CovEffects │ │ │ ├── sim_14.mcmcsamples.Par │ │ │ ├── sim_14.parRes │ │ │ ├── sim_14.snpRes │ │ │ ├── sim_15.covRes │ │ │ ├── sim_15.log │ │ │ ├── sim_15.mcmcsamples.CovEffects │ │ │ ├── sim_15.mcmcsamples.Par │ │ │ ├── sim_15.parRes │ │ │ ├── sim_15.snpRes │ │ │ ├── sim_16.covRes │ │ │ ├── sim_16.log │ │ │ ├── sim_16.mcmcsamples.CovEffects │ │ │ ├── sim_16.mcmcsamples.Par │ │ │ ├── sim_16.parRes │ │ │ ├── sim_16.snpRes │ │ │ ├── sim_17.covRes │ │ │ ├── sim_17.log │ │ │ ├── sim_17.mcmcsamples.CovEffects │ │ │ ├── sim_17.mcmcsamples.Par │ │ │ ├── sim_17.parRes │ │ │ ├── sim_17.snpRes │ │ │ ├── sim_18.covRes │ │ │ ├── sim_18.log │ │ │ ├── sim_18.mcmcsamples.CovEffects │ │ │ ├── sim_18.mcmcsamples.Par │ │ │ ├── sim_18.parRes │ │ │ ├── sim_18.snpRes │ │ │ ├── sim_19.covRes │ │ │ ├── sim_19.log │ │ │ ├── sim_19.mcmcsamples.CovEffects │ │ │ ├── sim_19.mcmcsamples.Par │ │ │ ├── sim_19.parRes │ │ │ ├── sim_19.snpRes │ │ │ ├── sim_2.covRes │ │ │ ├── sim_2.log │ │ │ ├── sim_2.mcmcsamples.CovEffects │ │ │ ├── sim_2.mcmcsamples.Par │ │ │ ├── sim_2.parRes │ │ │ ├── sim_2.snpRes │ │ │ ├── sim_20.covRes │ │ │ ├── sim_20.log │ │ │ ├── sim_20.mcmcsamples.CovEffects │ │ │ ├── sim_20.mcmcsamples.Par │ │ │ ├── sim_20.parRes │ │ │ ├── sim_20.snpRes │ │ │ ├── sim_3.covRes │ │ │ ├── sim_3.log │ │ │ ├── sim_3.mcmcsamples.CovEffects │ │ │ ├── sim_3.mcmcsamples.Par │ │ │ ├── sim_3.parRes │ │ │ ├── sim_3.snpRes │ │ │ ├── sim_4.covRes │ │ │ ├── sim_4.log │ │ │ ├── sim_4.mcmcsamples.CovEffects │ │ │ ├── sim_4.mcmcsamples.Par │ │ │ ├── sim_4.parRes │ │ │ ├── sim_4.snpRes │ │ │ ├── sim_5.covRes │ │ │ ├── sim_5.log │ │ │ ├── sim_5.mcmcsamples.CovEffects │ │ │ ├── sim_5.mcmcsamples.Par │ │ │ ├── sim_5.parRes │ │ │ ├── sim_5.snpRes │ │ │ ├── sim_6.covRes │ │ │ ├── sim_6.log │ │ │ ├── sim_6.mcmcsamples.CovEffects │ │ │ ├── sim_6.mcmcsamples.Par │ │ │ ├── sim_6.parRes │ │ │ ├── sim_6.snpRes │ │ │ ├── sim_7.covRes │ │ │ ├── sim_7.log │ │ │ ├── sim_7.mcmcsamples.CovEffects │ │ │ ├── sim_7.mcmcsamples.Par │ │ │ ├── sim_7.parRes │ │ │ ├── sim_7.snpRes │ │ │ ├── sim_8.covRes │ │ │ ├── sim_8.log │ │ │ ├── sim_8.mcmcsamples.CovEffects │ │ │ ├── sim_8.mcmcsamples.Par │ │ │ ├── sim_8.parRes │ │ │ ├── sim_8.snpRes │ │ │ ├── sim_9.covRes │ │ │ ├── sim_9.log │ │ │ ├── sim_9.mcmcsamples.CovEffects │ │ │ ├── sim_9.mcmcsamples.Par │ │ │ ├── sim_9.parRes │ │ │ ├── sim_9.snpRes │ │ │ └── submit_gctb_1000G_eur.job │ │ │ ├── gctb_out_r_1000G_eur_sparse │ │ │ ├── sim_1.covRes │ │ │ ├── sim_1.log │ │ │ ├── sim_1.mcmcsamples.CovEffects │ │ │ ├── sim_1.mcmcsamples.Par │ │ │ ├── sim_1.parRes │ │ │ ├── sim_1.snpRes │ │ │ ├── sim_10.covRes │ │ │ ├── sim_10.log │ │ │ ├── sim_10.mcmcsamples.CovEffects │ │ │ ├── sim_10.mcmcsamples.Par │ │ │ ├── sim_10.parRes │ │ │ ├── sim_10.snpRes │ │ │ ├── sim_11.covRes │ │ │ ├── sim_11.log │ │ │ ├── sim_11.mcmcsamples.CovEffects │ │ │ ├── sim_11.mcmcsamples.Par │ │ │ ├── sim_11.parRes │ │ │ ├── sim_11.snpRes │ │ │ ├── sim_12.covRes │ │ │ ├── sim_12.log │ │ │ ├── sim_12.mcmcsamples.CovEffects │ │ │ ├── sim_12.mcmcsamples.Par │ │ │ ├── sim_12.parRes │ │ │ ├── sim_12.snpRes │ │ │ ├── sim_13.covRes │ │ │ ├── sim_13.log │ │ │ ├── sim_13.mcmcsamples.CovEffects │ │ │ ├── sim_13.mcmcsamples.Par │ │ │ ├── sim_13.parRes │ │ │ ├── sim_13.snpRes │ │ │ ├── sim_14.covRes │ │ │ ├── sim_14.log │ │ │ ├── sim_14.mcmcsamples.CovEffects │ │ │ ├── sim_14.mcmcsamples.Par │ │ │ ├── sim_14.parRes │ │ │ ├── sim_14.snpRes │ │ │ ├── sim_15.covRes │ │ │ ├── sim_15.log │ │ │ ├── sim_15.mcmcsamples.CovEffects │ │ │ ├── sim_15.mcmcsamples.Par │ │ │ ├── sim_15.parRes │ │ │ ├── sim_15.snpRes │ │ │ ├── sim_16.covRes │ │ │ ├── sim_16.log │ │ │ ├── sim_16.mcmcsamples.CovEffects │ │ │ ├── sim_16.mcmcsamples.Par │ │ │ ├── sim_16.parRes │ │ │ ├── sim_16.snpRes │ │ │ ├── sim_17.covRes │ │ │ ├── sim_17.log │ │ │ ├── sim_17.mcmcsamples.CovEffects │ │ │ ├── sim_17.mcmcsamples.Par │ │ │ ├── sim_17.parRes │ │ │ ├── sim_17.snpRes │ │ │ ├── sim_18.covRes │ │ │ ├── sim_18.log │ │ │ ├── sim_18.mcmcsamples.CovEffects │ │ │ ├── sim_18.mcmcsamples.Par │ │ │ ├── sim_18.parRes │ │ │ ├── sim_18.snpRes │ │ │ ├── sim_19.covRes │ │ │ ├── sim_19.log │ │ │ ├── sim_19.mcmcsamples.CovEffects │ │ │ ├── sim_19.mcmcsamples.Par │ │ │ ├── sim_19.parRes │ │ │ ├── sim_19.snpRes │ │ │ ├── sim_2.covRes │ │ │ ├── sim_2.log │ │ │ ├── sim_2.mcmcsamples.CovEffects │ │ │ ├── sim_2.mcmcsamples.Par │ │ │ ├── sim_2.parRes │ │ │ ├── sim_2.snpRes │ │ │ ├── sim_20.covRes │ │ │ ├── sim_20.log │ │ │ ├── sim_20.mcmcsamples.CovEffects │ │ │ ├── sim_20.mcmcsamples.Par │ │ │ ├── sim_20.parRes │ │ │ ├── sim_20.snpRes │ │ │ ├── sim_3.covRes │ │ │ ├── sim_3.log │ │ │ ├── sim_3.mcmcsamples.CovEffects │ │ │ ├── sim_3.mcmcsamples.Par │ │ │ ├── sim_3.parRes │ │ │ ├── sim_3.snpRes │ │ │ ├── sim_4.covRes │ │ │ ├── sim_4.log │ │ │ ├── sim_4.mcmcsamples.CovEffects │ │ │ ├── sim_4.mcmcsamples.Par │ │ │ ├── sim_4.parRes │ │ │ ├── sim_4.snpRes │ │ │ ├── sim_5.covRes │ │ │ ├── sim_5.log │ │ │ ├── sim_5.mcmcsamples.CovEffects │ │ │ ├── sim_5.mcmcsamples.Par │ │ │ ├── sim_5.parRes │ │ │ ├── sim_5.snpRes │ │ │ ├── sim_6.covRes │ │ │ ├── sim_6.log │ │ │ ├── sim_6.mcmcsamples.CovEffects │ │ │ ├── sim_6.mcmcsamples.Par │ │ │ ├── sim_6.parRes │ │ │ ├── sim_6.snpRes │ │ │ ├── sim_7.covRes │ │ │ ├── sim_7.log │ │ │ ├── sim_7.mcmcsamples.CovEffects │ │ │ ├── sim_7.mcmcsamples.Par │ │ │ ├── sim_7.parRes │ │ │ ├── sim_7.snpRes │ │ │ ├── sim_8.covRes │ │ │ ├── sim_8.log │ │ │ ├── sim_8.mcmcsamples.CovEffects │ │ │ ├── sim_8.mcmcsamples.Par │ │ │ ├── sim_8.parRes │ │ │ ├── sim_8.snpRes │ │ │ ├── sim_9.covRes │ │ │ ├── sim_9.log │ │ │ ├── sim_9.mcmcsamples.CovEffects │ │ │ ├── sim_9.mcmcsamples.Par │ │ │ ├── sim_9.parRes │ │ │ ├── sim_9.snpRes │ │ │ └── submit_gctb_1000G_eur.job │ │ │ ├── gctb_submit_r_shrunk.sh │ │ │ └── gctb_submit_r_sparse.sh │ ├── gsmr │ │ ├── .gitattributes │ │ ├── Rplots.pdf │ │ ├── gsmr_example.bed │ │ ├── gsmr_example.bim │ │ ├── gsmr_example.corr │ │ ├── gsmr_example.fam │ │ ├── gsmr_example.recode.log │ │ ├── gsmr_example.xmat.gz │ │ └── gsmr_example_snps.allele │ ├── gwama │ │ ├── MANH.R │ │ ├── PLINK2GWAMA.pl │ │ ├── QQ.R │ │ ├── README.md │ │ ├── SNPTEST2.5_2_GWAMA.pl │ │ ├── SNPTEST2GWAMA.pl │ │ ├── SNPTEST2_2_GWAMA.pl │ │ ├── gwama.in │ │ ├── pop1.txt │ │ ├── pop2.txt │ │ └── pop3.txt │ ├── ldpred2 │ │ ├── .gitattributes │ │ ├── g1000_eur_chr21to22_hm3rnd1.bed │ │ ├── g1000_eur_chr21to22_hm3rnd1.bim │ │ ├── g1000_eur_chr21to22_hm3rnd1.fam │ │ ├── g1000_eur_chr21to22_hm3rnd1.log │ │ ├── g1000_eur_chr21to22_hm3rnd2.bed │ │ ├── g1000_eur_chr21to22_hm3rnd2.bim │ │ ├── g1000_eur_chr21to22_hm3rnd2.fam │ │ ├── g1000_eur_chr21to22_hm3rnd2.log │ │ ├── hm3_rand_v1.justrs │ │ ├── hm3_rand_v2.justrs │ │ ├── map_hm3_plus.justrs │ │ ├── simu.1.causals │ │ ├── simu.log │ │ ├── simu.pheno │ │ └── trait1.sumstats.gz │ ├── prsice2 │ │ ├── .gitattributes │ │ ├── EUR.bed │ │ ├── EUR.bim │ │ ├── EUR.cov │ │ ├── EUR.eigenvec │ │ ├── EUR.fam │ │ ├── EUR.height │ │ ├── Height.gwas.txt.gz │ │ ├── PRSice.R │ │ ├── README.txt │ │ ├── TOY_BASE_GWAS.assoc │ │ ├── TOY_TARGET_DATA.bed │ │ ├── TOY_TARGET_DATA.bim │ │ ├── TOY_TARGET_DATA.fam │ │ └── TOY_TARGET_DATA.pheno │ └── regenie │ │ ├── .gitattributes │ │ ├── README.md │ │ ├── covariates.txt │ │ ├── covariates.txt.gz │ │ ├── covariates_wBin.txt │ │ ├── example.bed │ │ ├── example.bgen │ │ ├── example.bgen.bgi │ │ ├── example.bim │ │ ├── example.fam │ │ ├── example.pgen │ │ ├── example.psam │ │ ├── example.pvar │ │ ├── example.test_bin_out_firth_Y1.regenie │ │ ├── example_3chr.annotations │ │ ├── example_3chr.annotationsV2 │ │ ├── example_3chr.argsfile │ │ ├── example_3chr.bed │ │ ├── example_3chr.bgen │ │ ├── example_3chr.bgen.bgi │ │ ├── example_3chr.bim │ │ ├── example_3chr.fam │ │ ├── example_3chr.info │ │ ├── example_3chr.joint_setlist │ │ ├── example_3chr.masks │ │ ├── example_3chr.pgen │ │ ├── example_3chr.pgrs.argsfile │ │ ├── example_3chr.pheno │ │ ├── example_3chr.pheno.dict │ │ ├── example_3chr.psam │ │ ├── example_3chr.pvar │ │ ├── example_3chr.sample │ │ ├── example_3chr.setlist │ │ ├── example_3chr.vcf.gz │ │ ├── example_3chr.vcf.gz.csi │ │ ├── example_3chr.vcf.gz.tbi │ │ ├── example_3chr.write_sets │ │ ├── example_3chr_bgen.argsfile │ │ ├── example_3chr_masks.bed │ │ ├── example_3chr_masks.bim │ │ ├── example_3chr_masks.fam │ │ ├── example_3chr_pgen.argsfile │ │ ├── example_3chr_vcf.argsfile │ │ ├── example_3chr_zstd.bgen │ │ ├── fid_iid_to_remove.txt │ │ ├── phenotype.txt │ │ ├── phenotype_bin.txt │ │ ├── phenotype_bin.txt.gz │ │ ├── phenotype_bin_wNA.txt │ │ └── snplist_rm.txt ├── hapgen │ ├── chr21.bed │ ├── chr21.bim │ └── chr21.fam ├── hapmap3 │ ├── .gitattributes │ ├── README.md │ └── w_hm3.justrs ├── hrc │ ├── HRC.r1-1.GRCh37.wgs.mac5.sites.tab.gz │ ├── README │ └── README.md └── sumstats │ ├── 50_irnt.gwas.imputed_v3.both_sexes.clean.about.txt │ ├── 50_irnt.gwas.imputed_v3.both_sexes.clean.tsv.gz │ ├── CHECKSUM_SavageJansen_2018_intelligence_metaanalysis.txt │ ├── Morningness_sumstats_Jansenetal.txt.gz │ ├── README.md │ ├── README_SavageJansen_2018_intelligence_metaanalysis.txt │ ├── SavageJansen_2018_intelligence_metaanalysis.txt.gz │ ├── clozuk_pgc2.meta.sumstats.README.txt │ └── clozuk_pgc2.meta.sumstats.txt.gz ├── scripts ├── README.md ├── gwas │ ├── README.md │ ├── config.yaml │ └── gwas.py └── pgs │ ├── LDpred2 │ ├── README.md │ ├── analyzeLD.R │ ├── calculateLD.R │ ├── complementSumstats.R │ ├── createBackingFile.R │ ├── fun.R │ ├── funMatrix.R │ ├── imputeGenotypes.R │ ├── ldpred2.R │ ├── ldpred2_simulations.ipynb │ ├── run_ldpred2_slurm.job │ └── splitLD.R │ ├── README.md │ └── pgs_toolkit │ ├── README.md │ ├── Rscripts │ ├── PRSice.R │ ├── README.md │ ├── create_QC_valid.R │ ├── create_valid_sample.R │ ├── evaluate_model.R │ ├── extract_columns.R │ ├── find_best_fit_pgs.R │ ├── generate_covariate.R │ ├── generate_eigenvec.R │ ├── strand_flipping.R │ └── update_effect_size.R │ ├── config.yaml │ ├── config_p697.yaml │ ├── pgs │ └── pgs.py │ ├── pgs_exec.py │ ├── pgs_exec_example_1.sh │ ├── pgs_exec_example_2.sh │ ├── pgs_exec_example_3.sh │ ├── pgs_exec_example_4.sh │ ├── requirements.txt │ ├── run_pgs_MoBa_LDpred2_auto.py │ ├── run_pgs_MoBa_LDpred2_inf.py │ ├── run_pgs_MoBa_plink.py │ ├── run_pgs_MoBa_prsice2.py │ ├── run_pgs_synthetic.py │ ├── run_pgs_w_QC.py │ ├── start_jupyter_server.py │ ├── tests │ └── __init__.py │ ├── vis_pgs_MoBa_height_8y_rint.ipynb │ ├── vis_pgs_synthetic.ipynb │ └── vis_pgs_w_QC.ipynb ├── specifications ├── geno_specification.md ├── pheno_specification.md └── sumstats_specification.md ├── sphinx-docs └── source │ ├── API.md │ ├── CHANGELOG.md │ ├── CONTRIBUTING.md │ ├── GETTING_STARTED.md │ ├── INSTALL.md │ ├── INTERNAL.md │ ├── INTRODUCTION.md │ ├── MAIN.md │ ├── Makefile │ ├── conf.py │ ├── containers │ ├── README.md │ └── external.md │ ├── docker │ └── README.md │ ├── docs │ ├── README.md │ ├── containers │ │ ├── README.md │ │ ├── gwas.md │ │ ├── hello.md │ │ ├── python3.md │ │ └── r.md │ └── singularity │ │ ├── README.md │ │ ├── gwas.md │ │ ├── hello.md │ │ ├── python3.md │ │ └── r.md │ ├── environment.yml │ ├── index.rst │ ├── make.bat │ ├── reference │ ├── README.md │ ├── opensnp.md │ └── sumstats │ │ └── README.md │ ├── scripts │ ├── README.md │ ├── gwas │ │ └── README.md │ └── pgs │ │ └── LDpred2 │ │ └── README.md │ ├── specifications │ ├── README.md │ ├── geno_specification.md │ ├── pheno_specification.md │ └── sumstats_specification.md │ └── usecases │ ├── README.md │ ├── bolt-lmm_demo.md │ ├── gwas_demo.md │ ├── gwas_real.md │ └── meta_simu.md ├── test-requirements.txt ├── tests ├── extras │ ├── GlucoseExample.tar.gz │ ├── bigsnpr.R │ ├── cars.R │ ├── cars.Rmd │ ├── ex.tar.gz │ ├── fastlmm_example_script.py │ └── r.R ├── test_LDpred2 │ ├── .gitignore │ ├── README.md │ ├── data │ │ ├── README │ │ ├── individual-ids.txt │ │ └── tutorial_data │ │ │ ├── public-data3-sumstats.txt │ │ │ ├── public-data3.bed │ │ │ ├── public-data3.bim │ │ │ └── public-data3.fam │ ├── maps │ │ └── README │ ├── output │ │ └── README │ ├── run.sh │ ├── scripts │ │ ├── backingfile.sh │ │ ├── extended.sh │ │ ├── functions.sh │ │ ├── imputation.sh │ │ ├── ld.sh │ │ ├── opensnp.sh │ │ ├── sumstats.sh │ │ └── tutorial.sh │ ├── temp │ │ └── README │ └── unittest │ │ ├── data │ │ ├── hrc37.txt │ │ └── sumstats.txt │ │ ├── extended.R │ │ ├── fun.R │ │ ├── funMatrix.R │ │ ├── ld.R │ │ └── tutorial.R ├── test_gwas.py ├── test_gwas_py.py ├── test_hello.py ├── test_python3.py └── test_r.py ├── usecases ├── README.md ├── bolt-lmm_demo.md ├── bolt_out │ ├── .gitattributes │ ├── example_3chr.LDSCORE.tab │ ├── example_3chr.frq │ ├── example_3chr.lmm.pheno │ ├── example_3chr.log │ ├── example_3chr.nosex │ ├── example_3chr.snplist │ ├── example_3chr_bolt.stats │ ├── myld.l2.M │ ├── myld.l2.M_5_50 │ ├── myld.l2.ldscore.gz │ └── myld.log ├── gwas_demo.md ├── gwas_demo │ ├── .gitattributes │ ├── run1.covar │ ├── run1.log │ ├── run1.pheno │ ├── run1.regenie.step1.log │ ├── run1.regenie.step1_1.loco │ ├── run1.regenie.step1_2.loco │ ├── run1.regenie.step1_pred.list │ ├── run1_CASE.plink2.gz │ ├── run1_CASE.plink2.log │ ├── run1_CASE.regenie.gz │ ├── run1_CASE.regenie.log │ ├── run1_CASE2.plink2.gz │ ├── run1_CASE2.plink2.log │ ├── run1_CASE2.regenie.gz │ ├── run1_CASE2.regenie.log │ ├── run1_chr1.CASE.glm.logistic │ ├── run1_chr1.CASE2.glm.logistic │ ├── run1_chr1.log │ ├── run1_chr1_CASE.regenie │ ├── run1_chr1_CASE2.regenie │ ├── run1_chr2.CASE.glm.logistic │ ├── run1_chr2.CASE2.glm.logistic │ ├── run1_chr2.log │ ├── run1_chr2_CASE.regenie │ ├── run1_chr2_CASE2.regenie │ ├── run1_chr3.CASE.glm.logistic │ ├── run1_chr3.CASE2.glm.logistic │ ├── run1_chr3.log │ ├── run1_chr3_CASE.regenie │ ├── run1_chr3_CASE2.regenie │ ├── run1_cmd.sh │ ├── run1_plink2.1.job │ ├── run1_plink2.2.job │ ├── run1_regenie.1.job │ ├── run1_regenie.2.job │ ├── run1_regenie.3.job │ ├── run2.covar │ ├── run2.log │ ├── run2.pheno │ ├── run2.regenie.step1.log │ ├── run2.regenie.step1_1.loco │ ├── run2.regenie.step1_2.loco │ ├── run2.regenie.step1_pred.list │ ├── run2_PHENO.plink2.gz │ ├── run2_PHENO.plink2.log │ ├── run2_PHENO.regenie.gz │ ├── run2_PHENO.regenie.log │ ├── run2_PHENO2.plink2.gz │ ├── run2_PHENO2.plink2.log │ ├── run2_PHENO2.regenie.gz │ ├── run2_PHENO2.regenie.log │ ├── run2_chr1.PHENO.glm.linear │ ├── run2_chr1.PHENO2.glm.linear │ ├── run2_chr1.log │ ├── run2_chr1_PHENO.regenie │ ├── run2_chr1_PHENO2.regenie │ ├── run2_chr2.PHENO.glm.linear │ ├── run2_chr2.PHENO2.glm.linear │ ├── run2_chr2.log │ ├── run2_chr2_PHENO.regenie │ ├── run2_chr2_PHENO2.regenie │ ├── run2_chr3.PHENO.glm.linear │ ├── run2_chr3.PHENO2.glm.linear │ ├── run2_chr3.log │ ├── run2_chr3_PHENO.regenie │ ├── run2_chr3_PHENO2.regenie │ ├── run2_cmd.sh │ ├── run2_plink2.1.job │ ├── run2_plink2.2.job │ ├── run2_regenie.1.job │ ├── run2_regenie.2.job │ └── run2_regenie.3.job ├── gwas_real.md ├── gwas_real │ ├── combine_figures.py │ ├── dep.qq.png │ ├── height.qq.png │ ├── moba.bed.argsfile │ ├── moba.bgen.argsfile │ ├── moba.pheno.dict │ ├── run1_height.plink2.gz.manh.png │ ├── run1_height.plink2.gz.qq.png │ ├── run1_height.plink2.gz.qq.png.json │ ├── run2_height.regenie.gz.manh.png │ ├── run2_height.regenie.gz.qq.png │ ├── run2_height.regenie.gz.qq.png.json │ ├── run3_AnyF32.plink2.gz.manh.png │ ├── run3_AnyF32.plink2.gz.qq.png │ ├── run3_AnyF32.plink2.gz.qq.png.json │ ├── run3_AnyF33.plink2.gz.manh.png │ ├── run3_AnyF33.plink2.gz.qq.png │ ├── run3_AnyF33.plink2.gz.qq.png.json │ ├── run3_AnyFdep.plink2.gz.manh.png │ ├── run3_AnyFdep.plink2.gz.qq.png │ ├── run3_AnyFdep.plink2.gz.qq.png.json │ ├── run4_AnyF32.regenie.gz.manh.png │ ├── 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