├── .dockerignore ├── usecases ├── bolt_out │ ├── myld.l2.M │ ├── myld.l2.M_5_50 │ ├── .gitattributes │ ├── myld.log │ ├── example_3chr.frq │ ├── example_3chr.log │ └── myld.l2.ldscore.gz ├── gwas_real │ ├── dep.qq.png │ ├── height.qq.png │ ├── run1_height.plink2.gz.qq.png │ ├── run2_height.regenie.gz.qq.png │ ├── run3_AnyF32.plink2.gz.qq.png │ ├── run3_AnyF33.plink2.gz.qq.png │ ├── run3_AnyFdep.plink2.gz.qq.png │ ├── run4_AnyF32.regenie.gz.qq.png │ ├── run4_AnyF33.regenie.gz.qq.png │ ├── run5_height.plink2.gz.qq.png │ ├── run6_height.regenie.gz.qq.png │ ├── run7_AnyF32.plink2.gz.qq.png │ ├── run7_AnyF33.plink2.gz.qq.png │ ├── run7_AnyFdep.plink2.gz.qq.png │ ├── run8_AnyF32.regenie.gz.qq.png │ ├── run8_AnyF33.regenie.gz.qq.png │ ├── run1_height.plink2.gz.manh.png │ ├── run2_height.regenie.gz.manh.png │ ├── run3_AnyF32.plink2.gz.manh.png │ ├── run3_AnyF33.plink2.gz.manh.png │ ├── run3_AnyFdep.plink2.gz.manh.png │ ├── run4_AnyF32.regenie.gz.manh.png │ ├── run4_AnyF33.regenie.gz.manh.png │ ├── run4_AnyFdep.regenie.gz.manh.png │ ├── run4_AnyFdep.regenie.gz.qq.png │ ├── run5_height.plink2.gz.manh.png │ ├── run6_height.regenie.gz.manh.png │ ├── run7_AnyF32.plink2.gz.manh.png │ ├── run7_AnyF33.plink2.gz.manh.png │ ├── run7_AnyFdep.plink2.gz.manh.png │ ├── run8_AnyF32.regenie.gz.manh.png │ ├── run8_AnyF33.regenie.gz.manh.png │ ├── run8_AnyFdep.regenie.gz.manh.png │ ├── run8_AnyFdep.regenie.gz.qq.png │ ├── moba.bgen.argsfile │ └── moba.bed.argsfile ├── gwas_demo │ ├── run1.regenie.step1_pred.list │ ├── run2.regenie.step1_pred.list │ ├── run1.log │ ├── run2.log │ ├── run1_chr1.log │ ├── run1_chr2.log │ ├── run1_chr3.log │ ├── run2_chr1.log │ ├── run2_chr2.log │ ├── run2_chr3.log │ ├── run1.regenie.step1.log │ ├── 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 │ ├── run2.regenie.step1.log │ ├── 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 └── pgs │ └── README.md ├── scripts ├── pgs │ ├── pgs_toolkit │ │ ├── tests │ │ │ └── __init__.py │ │ ├── requirements.txt │ │ └── Rscripts │ │ │ ├── README.md │ │ │ └── update_effect_size.R │ └── README.md ├── README.md └── gwas │ └── README.md ├── tests ├── extras │ ├── cars.R │ ├── ex.tar.gz │ └── GlucoseExample.tar.gz └── test_LDpred2 │ ├── temp │ └── README │ ├── maps │ └── README │ ├── output │ └── README │ ├── data │ ├── tutorial_data │ │ ├── public-data3.bed │ │ ├── public-data3.bim │ │ └── public-data3.fam │ └── README │ └── .gitignore ├── sphinx-docs └── source │ ├── INSTALL.md │ ├── CHANGELOG.md │ ├── CONTRIBUTING.md │ ├── docker │ └── README.md │ ├── docs │ ├── README.md │ ├── containers │ │ ├── r.md │ │ ├── gwas.md │ │ ├── README.md │ │ ├── hello.md │ │ └── python3.md │ └── singularity │ │ ├── r.md │ │ ├── README.md │ │ ├── gwas.md │ │ ├── hello.md │ │ └── python3.md │ ├── scripts │ ├── gwas │ │ └── README.md │ ├── pgs │ │ └── LDpred2 │ │ │ └── README.md │ └── README.md │ ├── usecases │ ├── gwas_demo.md │ ├── meta_simu.md │ ├── bolt-lmm_demo.md │ ├── gwas_real.md │ └── README.md │ ├── reference │ ├── sumstats │ │ └── README.md │ ├── README.md │ └── opensnp.md │ ├── specifications │ ├── geno_specification.md │ ├── pheno_specification.md │ ├── sumstats_specification.md │ └── README.md │ ├── INTERNAL.md │ ├── INTRODUCTION.md │ ├── API.md │ ├── GETTING_STARTED.md │ ├── MAIN.md │ ├── environment.yml │ └── containers │ └── README.md ├── pytest.ini ├── reference ├── examples │ ├── gwama │ │ ├── gwama.in │ │ └── pop1.txt │ ├── regenie │ │ ├── example_3chr.write_sets │ │ ├── snplist_rm.txt │ │ ├── example_3chr.masks │ │ ├── fid_iid_to_remove.txt │ │ ├── example.bed │ │ ├── example.bgen │ │ ├── example.bim │ │ ├── example.fam │ │ ├── example.pgen │ │ ├── covariates.txt.gz │ │ ├── example.bgen.bgi │ │ ├── example_3chr.bed │ │ ├── example_3chr.bgen │ │ ├── example_3chr.bim │ │ ├── example_3chr.fam │ │ ├── example_3chr.pgen │ │ ├── example_3chr.psam │ │ ├── example_3chr.pvar │ │ ├── example_3chr.vcf.gz │ │ ├── example_3chr_masks.bim │ │ ├── phenotype_bin.txt.gz │ │ ├── example_3chr.bgen.bgi │ │ ├── example_3chr.vcf.gz.csi │ │ ├── example_3chr.vcf.gz.tbi │ │ ├── example_3chr_masks.bed │ │ ├── example_3chr_masks.fam │ │ ├── example_3chr_zstd.bgen │ │ ├── example.test_bin_out_firth_Y1.regenie │ │ ├── example_3chr.joint_setlist │ │ ├── example_3chr.pgrs.argsfile │ │ ├── example_3chr_bgen.argsfile │ │ ├── example_3chr_pgen.argsfile │ │ ├── example_3chr.argsfile │ │ ├── example_3chr.pheno.dict │ │ └── example_3chr_vcf.argsfile │ ├── gsmr │ │ ├── Rplots.pdf │ │ ├── gsmr_example.bed │ │ ├── gsmr_example.bim │ │ ├── gsmr_example.fam │ │ ├── gsmr_example.recode.log │ │ ├── gsmr_example.xmat.gz │ │ └── .gitattributes │ ├── gctb_2.0_tutorial │ │ ├── data │ │ │ ├── .DS_Store │ │ │ ├── 1000G_eur_chr22.fam │ │ │ ├── 1000G_eur_chr22.bed │ │ │ ├── 1000G_eur_chr22.bim │ │ │ └── 1000G_eur_chr22.freq │ │ ├── gwas │ │ │ ├── sim_1.log │ │ │ ├── sim_10.log │ │ │ ├── sim_11.log │ │ │ ├── sim_12.log │ │ │ ├── sim_13.log │ │ │ ├── sim_14.log │ │ │ ├── sim_15.log │ │ │ ├── sim_16.log │ │ │ ├── sim_17.log │ │ │ ├── sim_18.log │ │ │ ├── sim_19.log │ │ │ ├── sim_2.log │ │ │ ├── sim_20.log │ │ │ ├── sim_3.log │ │ │ ├── sim_4.log │ │ │ ├── sim_5.log │ │ │ ├── sim_6.log │ │ │ ├── sim_7.log │ │ │ ├── sim_8.log │ │ │ ├── sim_9.log │ │ │ ├── sim_1.assoc.linear │ │ │ ├── sim_10.assoc.linear │ │ │ ├── sim_11.assoc.linear │ │ │ ├── sim_12.assoc.linear │ │ │ ├── sim_13.assoc.linear │ │ │ ├── sim_14.assoc.linear │ │ │ ├── sim_15.assoc.linear │ │ │ ├── sim_16.assoc.linear │ │ │ ├── sim_17.assoc.linear │ │ │ ├── sim_18.assoc.linear │ │ │ ├── sim_19.assoc.linear │ │ │ ├── sim_2.assoc.linear │ │ │ ├── sim_20.assoc.linear │ │ │ ├── sim_3.assoc.linear │ │ │ ├── sim_4.assoc.linear │ │ │ ├── sim_5.assoc.linear │ │ │ ├── sim_6.assoc.linear │ │ │ ├── sim_7.assoc.linear │ │ │ ├── sim_8.assoc.linear │ │ │ ├── sim_9.assoc.linear │ │ │ └── plink_submit_combination.sh │ │ ├── ma │ │ │ ├── ma_create.R │ │ │ ├── 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 │ │ │ └── ma_create_submit.sh │ │ ├── about.txt │ │ ├── ldm │ │ │ ├── makeldm_full.sh │ │ │ ├── makeldm_shrunk.sh │ │ │ ├── makeldm_sparse.sh │ │ │ ├── makeldm_full_mcpu.sh │ │ │ ├── makeldm_shrunk_mcpu.sh │ │ │ ├── merge_full_mcpu.sh │ │ │ ├── merge_shrunk_mcpu.sh │ │ │ ├── shrunk │ │ │ │ └── chr22 │ │ │ │ │ ├── makeldm.job │ │ │ │ │ ├── make_shrunk_sparse.sh │ │ │ │ │ ├── 1000G_eur_chr22.ldm.shrunk.log │ │ │ │ │ ├── 1000G_eur_chr22.ldm.shrunk.info │ │ │ │ │ ├── 1000G_eur_chr22.ldm.sparse.bin │ │ │ │ │ └── 1000G_eur_chr22.ldm.sparse.info │ │ │ ├── shrunk_mcpu │ │ │ │ └── chr22 │ │ │ │ │ ├── merge.job │ │ │ │ │ ├── makeldm.job │ │ │ │ │ ├── merge.pbspro │ │ │ │ │ ├── merge_1.pbspro │ │ │ │ │ ├── merge_2.pbspro │ │ │ │ │ ├── 1000G_eur_chr22.log │ │ │ │ │ ├── 1000G_eur_chr22.mldmlist │ │ │ │ │ ├── 1000G_eur_chr22.ldm.shrunk.info │ │ │ │ │ ├── 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 │ │ │ ├── sparse │ │ │ │ └── chr22 │ │ │ │ │ ├── makeldm.job │ │ │ │ │ ├── 1000G_eur_chr22.ldm.sparse.log │ │ │ │ │ ├── 1000G_eur_chr22.ldm.sparse.bin │ │ │ │ │ └── 1000G_eur_chr22.ldm.sparse.info │ │ │ └── genetic_map │ │ │ │ └── chr22.OMNI.interpolated_genetic_map │ │ ├── pheno │ │ │ ├── phenos_ga1.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 │ │ │ ├── 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 │ │ ├── sbayesr │ │ │ ├── gctb_submit_r_shrunk.sh │ │ │ ├── gctb_submit_r_sparse.sh │ │ │ ├── gctb_out_r_1000G_eur_shrunk │ │ │ │ ├── sim_1.covRes │ │ │ │ ├── sim_1.log │ │ │ │ ├── sim_1.parRes │ │ │ │ ├── sim_10.covRes │ │ │ │ ├── sim_10.log │ │ │ │ ├── sim_10.parRes │ │ │ │ ├── sim_11.covRes │ │ │ │ ├── sim_11.log │ │ │ │ ├── sim_11.parRes │ │ │ │ ├── sim_12.covRes │ │ │ │ ├── sim_12.log │ │ │ │ ├── sim_12.parRes │ │ │ │ ├── sim_13.covRes │ │ │ │ ├── sim_13.log │ │ │ │ ├── sim_13.parRes │ │ │ │ ├── sim_14.covRes │ │ │ │ ├── sim_14.log │ │ │ │ ├── sim_14.parRes │ │ │ │ ├── sim_15.covRes │ │ │ │ ├── sim_15.log │ │ │ │ ├── sim_15.parRes │ │ │ │ ├── sim_16.covRes │ │ │ │ ├── sim_16.log │ │ │ │ ├── sim_16.parRes │ │ │ │ ├── sim_17.covRes │ │ │ │ ├── sim_17.log │ │ │ │ ├── sim_17.parRes │ │ │ │ ├── sim_18.covRes │ │ │ │ ├── sim_18.log │ │ │ │ ├── sim_18.parRes │ │ │ │ ├── sim_19.covRes │ │ │ │ ├── sim_19.log │ │ │ │ ├── sim_19.parRes │ │ │ │ ├── sim_2.covRes │ │ │ │ ├── sim_2.log │ │ │ │ ├── sim_2.parRes │ │ │ │ ├── sim_20.covRes │ │ │ │ ├── sim_20.log │ │ │ │ ├── sim_20.parRes │ │ │ │ ├── sim_3.covRes │ │ │ │ ├── sim_3.log │ │ │ │ ├── sim_3.parRes │ │ │ │ ├── sim_4.covRes │ │ │ │ ├── sim_4.log │ │ │ │ ├── sim_4.parRes │ │ │ │ ├── sim_5.covRes │ │ │ │ ├── sim_5.log │ │ │ │ ├── sim_5.parRes │ │ │ │ ├── sim_6.covRes │ │ │ │ ├── sim_6.log │ │ │ │ ├── sim_6.parRes │ │ │ │ ├── sim_7.covRes │ │ │ │ ├── sim_7.log │ │ │ │ ├── sim_7.parRes │ │ │ │ ├── sim_8.covRes │ │ │ │ ├── sim_8.log │ │ │ │ ├── sim_8.parRes │ │ │ │ ├── sim_9.covRes │ │ │ │ ├── sim_9.log │ │ │ │ ├── sim_9.parRes │ │ │ │ ├── sim_1.snpRes │ │ │ │ ├── sim_10.snpRes │ │ │ │ ├── sim_11.snpRes │ │ │ │ ├── sim_12.snpRes │ │ │ │ ├── sim_13.snpRes │ │ │ │ ├── sim_14.snpRes │ │ │ │ ├── sim_15.snpRes │ │ │ │ ├── sim_16.snpRes │ │ │ │ ├── sim_17.snpRes │ │ │ │ ├── sim_18.snpRes │ │ │ │ ├── sim_19.snpRes │ │ │ │ ├── sim_2.snpRes │ │ │ │ ├── sim_20.snpRes │ │ │ │ ├── sim_3.snpRes │ │ │ │ ├── sim_4.snpRes │ │ │ │ ├── sim_5.snpRes │ │ │ │ ├── sim_6.snpRes │ │ │ │ ├── sim_7.snpRes │ │ │ │ ├── sim_8.snpRes │ │ │ │ ├── sim_9.snpRes │ │ │ │ ├── sim_1.mcmcsamples.Par │ │ │ │ ├── sim_2.mcmcsamples.Par │ │ │ │ ├── sim_3.mcmcsamples.Par │ │ │ │ ├── sim_4.mcmcsamples.Par │ │ │ │ ├── sim_5.mcmcsamples.Par │ │ │ │ ├── sim_6.mcmcsamples.Par │ │ │ │ ├── sim_7.mcmcsamples.Par │ │ │ │ ├── sim_8.mcmcsamples.Par │ │ │ │ ├── sim_9.mcmcsamples.Par │ │ │ │ ├── submit_gctb_1000G_eur.job │ │ │ │ ├── sim_1.mcmcsamples.CovEffects │ │ │ │ ├── sim_10.mcmcsamples.Par │ │ │ │ ├── sim_11.mcmcsamples.Par │ │ │ │ ├── sim_12.mcmcsamples.Par │ │ │ │ ├── sim_13.mcmcsamples.Par │ │ │ │ ├── sim_14.mcmcsamples.Par │ │ │ │ ├── sim_15.mcmcsamples.Par │ │ │ │ ├── sim_16.mcmcsamples.Par │ │ │ │ ├── sim_17.mcmcsamples.Par │ │ │ │ ├── sim_18.mcmcsamples.Par │ │ │ │ ├── sim_19.mcmcsamples.Par │ │ │ │ ├── sim_2.mcmcsamples.CovEffects │ │ │ │ ├── sim_20.mcmcsamples.Par │ │ │ │ ├── sim_3.mcmcsamples.CovEffects │ │ │ │ ├── sim_4.mcmcsamples.CovEffects │ │ │ │ ├── sim_5.mcmcsamples.CovEffects │ │ │ │ ├── sim_6.mcmcsamples.CovEffects │ │ │ │ ├── sim_7.mcmcsamples.CovEffects │ │ │ │ ├── sim_8.mcmcsamples.CovEffects │ │ │ │ ├── sim_9.mcmcsamples.CovEffects │ │ │ │ ├── sim_10.mcmcsamples.CovEffects │ │ │ │ ├── sim_11.mcmcsamples.CovEffects │ │ │ │ ├── sim_12.mcmcsamples.CovEffects │ │ │ │ ├── sim_13.mcmcsamples.CovEffects │ │ │ │ ├── sim_14.mcmcsamples.CovEffects │ │ │ │ ├── sim_15.mcmcsamples.CovEffects │ │ │ │ ├── sim_16.mcmcsamples.CovEffects │ │ │ │ ├── sim_17.mcmcsamples.CovEffects │ │ │ │ ├── sim_18.mcmcsamples.CovEffects │ │ │ │ ├── sim_19.mcmcsamples.CovEffects │ │ │ │ └── sim_20.mcmcsamples.CovEffects │ │ │ └── gctb_out_r_1000G_eur_sparse │ │ │ │ ├── sim_1.covRes │ │ │ │ ├── sim_1.log │ │ │ │ ├── sim_1.parRes │ │ │ │ ├── sim_10.covRes │ │ │ │ ├── sim_10.log │ │ │ │ ├── sim_10.parRes │ │ │ │ ├── sim_11.covRes │ │ │ │ ├── sim_11.log │ │ │ │ ├── sim_11.parRes │ │ │ │ ├── sim_12.covRes │ │ │ │ ├── sim_12.log │ │ │ │ ├── sim_12.parRes │ │ │ │ ├── sim_13.covRes │ │ │ │ ├── sim_13.log │ │ │ │ ├── sim_13.parRes │ │ │ │ ├── sim_14.covRes │ │ │ │ ├── sim_14.log │ │ │ │ ├── sim_14.parRes │ │ │ │ ├── sim_15.covRes │ │ │ │ ├── sim_15.log │ │ │ │ ├── sim_15.parRes │ │ │ │ ├── sim_16.covRes │ │ │ │ ├── sim_16.log │ │ │ │ ├── sim_16.parRes │ │ │ │ ├── sim_17.covRes │ │ │ │ ├── sim_17.log │ │ │ │ ├── sim_17.parRes │ │ │ │ ├── sim_18.covRes │ │ │ │ ├── sim_18.log │ │ │ │ ├── sim_18.parRes │ │ │ │ ├── sim_19.covRes │ │ │ │ ├── sim_19.log │ │ │ │ ├── sim_19.parRes │ │ │ │ ├── sim_2.covRes │ │ │ │ ├── sim_2.log │ │ │ │ ├── sim_2.parRes │ │ │ │ ├── sim_20.covRes │ │ │ │ ├── sim_20.log │ │ │ │ ├── sim_20.parRes │ │ │ │ ├── sim_3.covRes │ │ │ │ ├── sim_3.log │ │ │ │ ├── sim_3.parRes │ │ │ │ ├── sim_4.covRes │ │ │ │ ├── sim_4.log │ │ │ │ ├── sim_4.parRes │ │ │ │ ├── sim_5.covRes │ │ │ │ ├── sim_5.log │ │ │ │ ├── sim_5.parRes │ │ │ │ ├── sim_6.covRes │ │ │ │ ├── sim_6.log │ │ │ │ ├── sim_6.parRes │ │ │ │ ├── sim_7.covRes │ │ │ │ ├── sim_7.log │ │ │ │ ├── sim_7.parRes │ │ │ │ ├── sim_8.covRes │ │ │ │ ├── sim_8.log │ │ │ │ ├── sim_8.parRes │ │ │ │ ├── sim_9.covRes │ │ │ │ ├── sim_9.log │ │ │ │ ├── sim_9.parRes │ │ │ │ ├── sim_1.snpRes │ │ │ │ ├── sim_10.snpRes │ │ │ │ ├── sim_11.snpRes │ │ │ │ ├── sim_12.snpRes │ │ │ │ ├── sim_13.snpRes │ │ │ │ ├── sim_14.snpRes │ │ │ │ ├── sim_15.snpRes │ │ │ │ ├── sim_16.snpRes │ │ │ │ ├── sim_17.snpRes │ │ │ │ ├── sim_18.snpRes │ │ │ │ ├── sim_19.snpRes │ │ │ │ ├── sim_2.snpRes │ │ │ │ ├── sim_20.snpRes │ │ │ │ ├── sim_3.snpRes │ │ │ │ ├── sim_4.snpRes │ │ │ │ ├── sim_5.snpRes │ │ │ │ ├── sim_6.snpRes │ │ │ │ ├── sim_7.snpRes │ │ │ │ ├── sim_8.snpRes │ │ │ │ ├── sim_9.snpRes │ │ │ │ ├── sim_1.mcmcsamples.Par │ │ │ │ ├── sim_2.mcmcsamples.Par │ │ │ │ ├── sim_3.mcmcsamples.Par │ │ │ │ ├── sim_4.mcmcsamples.Par │ │ │ │ ├── sim_5.mcmcsamples.Par │ │ │ │ ├── sim_6.mcmcsamples.Par │ │ │ │ ├── sim_7.mcmcsamples.Par │ │ │ │ ├── sim_8.mcmcsamples.Par │ │ │ │ ├── sim_9.mcmcsamples.Par │ │ │ │ ├── submit_gctb_1000G_eur.job │ │ │ │ ├── sim_1.mcmcsamples.CovEffects │ │ │ │ ├── sim_10.mcmcsamples.Par │ │ │ │ ├── sim_11.mcmcsamples.Par │ │ │ │ ├── sim_12.mcmcsamples.Par │ │ │ │ ├── sim_13.mcmcsamples.Par │ │ │ │ ├── sim_14.mcmcsamples.Par │ │ │ │ ├── sim_15.mcmcsamples.Par │ │ │ │ ├── sim_16.mcmcsamples.Par │ │ │ │ ├── sim_17.mcmcsamples.Par │ │ │ │ ├── sim_18.mcmcsamples.Par │ │ │ │ ├── sim_19.mcmcsamples.Par │ │ │ │ ├── sim_2.mcmcsamples.CovEffects │ │ │ │ ├── sim_20.mcmcsamples.Par │ │ │ │ ├── sim_3.mcmcsamples.CovEffects │ │ │ │ ├── sim_4.mcmcsamples.CovEffects │ │ │ │ ├── sim_5.mcmcsamples.CovEffects │ │ │ │ ├── sim_6.mcmcsamples.CovEffects │ │ │ │ ├── sim_7.mcmcsamples.CovEffects │ │ │ │ ├── sim_8.mcmcsamples.CovEffects │ │ │ │ ├── sim_9.mcmcsamples.CovEffects │ │ │ │ ├── sim_10.mcmcsamples.CovEffects │ │ │ │ ├── sim_11.mcmcsamples.CovEffects │ │ │ │ ├── sim_12.mcmcsamples.CovEffects │ │ │ │ ├── sim_13.mcmcsamples.CovEffects │ │ │ │ ├── sim_14.mcmcsamples.CovEffects │ │ │ │ ├── sim_15.mcmcsamples.CovEffects │ │ │ │ ├── sim_16.mcmcsamples.CovEffects │ │ │ │ ├── sim_17.mcmcsamples.CovEffects │ │ │ │ ├── sim_18.mcmcsamples.CovEffects │ │ │ │ ├── sim_19.mcmcsamples.CovEffects │ │ │ │ └── sim_20.mcmcsamples.CovEffects │ │ └── pheno_generation │ │ │ ├── pheno_generate.R │ │ │ ├── read_plink_func.R │ │ │ ├── 1000G_genos_scaled.Rdata │ │ │ ├── pheno_generate_validation.R │ │ │ └── ukb_eu_hm3_chr21_22_scaled.Rdata │ ├── ldpred2 │ │ ├── simu.log │ │ ├── simu.1.causals │ │ ├── simu.pheno │ │ ├── hm3_rand_v1.justrs │ │ ├── hm3_rand_v2.justrs │ │ ├── trait1.sumstats.gz │ │ ├── map_hm3_plus.justrs │ │ ├── g1000_eur_chr21to22_hm3rnd1.log │ │ ├── g1000_eur_chr21to22_hm3rnd2.log │ │ ├── g1000_eur_chr21to22_hm3rnd1.bed │ │ ├── g1000_eur_chr21to22_hm3rnd1.bim │ │ ├── g1000_eur_chr21to22_hm3rnd1.fam │ │ ├── g1000_eur_chr21to22_hm3rnd2.bed │ │ ├── g1000_eur_chr21to22_hm3rnd2.bim │ │ └── g1000_eur_chr21to22_hm3rnd2.fam │ └── prsice2 │ │ ├── EUR.cov │ │ ├── EUR.fam │ │ ├── EUR.bed │ │ ├── EUR.bim │ │ ├── EUR.eigenvec │ │ ├── EUR.height │ │ ├── TOY_TARGET_DATA.fam │ │ ├── Height.gwas.txt.gz │ │ ├── TOY_BASE_GWAS.assoc │ │ ├── TOY_TARGET_DATA.bed │ │ ├── TOY_TARGET_DATA.bim │ │ ├── TOY_TARGET_DATA.pheno │ │ └── README.txt ├── hapmap3 │ ├── .gitattributes │ ├── w_hm3.justrs │ └── README.md ├── sumstats │ ├── CHECKSUM_SavageJansen_2018_intelligence_metaanalysis.txt │ ├── clozuk_pgc2.meta.sumstats.txt.gz │ ├── Morningness_sumstats_Jansenetal.txt.gz │ ├── 50_irnt.gwas.imputed_v3.both_sexes.clean.tsv.gz │ └── SavageJansen_2018_intelligence_metaanalysis.txt.gz ├── hapgen │ ├── chr21.bed │ ├── chr21.bim │ └── chr21.fam └── hrc │ ├── README.md │ └── HRC.r1-1.GRCh37.wgs.mac5.sites.tab.gz ├── test-requirements.txt ├── docker ├── scripts │ ├── python_convert.sh │ ├── R │ │ └── source.R │ ├── install_liftover.sh │ ├── install_simu.sh │ ├── install_ldak.sh │ ├── install_gwama.sh │ ├── stub.sh │ ├── install_bedtools.sh │ ├── install_duohmm.sh │ ├── install_flashpca.sh │ ├── install_plink2.sh │ ├── install_plink.sh │ ├── install_gcta.sh │ ├── install_prsice.sh │ ├── install_snptest.sh │ ├── install_metal.sh │ ├── install_vcftools.sh │ ├── install_miniforge.sh │ ├── install_gctb.sh │ ├── install_bgenix.sh │ ├── install_plink2_avx2.sh │ ├── install_eagle.sh │ ├── install_beagle.sh │ ├── install_king.sh │ ├── patches │ │ └── shapeit4.makefile.diff │ ├── install_shapeit4.sh │ └── install_samtools.sh └── dockerfiles │ └── hello │ └── Dockerfile ├── containers └── README.md ├── environment.yml ├── .readthedocs.yml ├── .github ├── ISSUE_TEMPLATE │ └── documentation-issue.md └── workflows │ ├── greetings.yml │ └── docker.yml └── version └── version.py /.dockerignore: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /usecases/bolt_out/myld.l2.M: -------------------------------------------------------------------------------- 1 | 500 2 | -------------------------------------------------------------------------------- /scripts/pgs/pgs_toolkit/tests/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /usecases/bolt_out/myld.l2.M_5_50: -------------------------------------------------------------------------------- 1 | 490 2 | -------------------------------------------------------------------------------- /tests/extras/cars.R: -------------------------------------------------------------------------------- 1 | rmarkdown::render("cars.Rmd") -------------------------------------------------------------------------------- /tests/test_LDpred2/temp/README: -------------------------------------------------------------------------------- 1 | Temporary files 2 | -------------------------------------------------------------------------------- /scripts/pgs/pgs_toolkit/requirements.txt: -------------------------------------------------------------------------------- 1 | pandas 2 | pyyaml 3 | -------------------------------------------------------------------------------- /sphinx-docs/source/INSTALL.md: -------------------------------------------------------------------------------- 1 | ```{include} ../../INSTALL.md 2 | ``` 3 | -------------------------------------------------------------------------------- /tests/test_LDpred2/maps/README: -------------------------------------------------------------------------------- 1 | Genomic maps are currently stored here 2 | -------------------------------------------------------------------------------- /pytest.ini: -------------------------------------------------------------------------------- 1 | [pytest] 2 | addopts = --ignore=test_LDpred2 3 | testpaths = tests -------------------------------------------------------------------------------- /reference/examples/gwama/gwama.in: -------------------------------------------------------------------------------- 1 | pop1.txt 2 | pop2.txt 3 | pop3.txt 4 | -------------------------------------------------------------------------------- /reference/examples/regenie/example_3chr.write_sets: -------------------------------------------------------------------------------- 1 | tmp1 M1 2 | tmp2 M1,M2 3 | -------------------------------------------------------------------------------- /sphinx-docs/source/CHANGELOG.md: -------------------------------------------------------------------------------- 1 | ```{include} ../../CHANGELOG.md 2 | ``` 3 | -------------------------------------------------------------------------------- /test-requirements.txt: -------------------------------------------------------------------------------- 1 | # pip requirements file for running tests 2 | pytest 3 | -------------------------------------------------------------------------------- /tests/test_LDpred2/output/README: -------------------------------------------------------------------------------- 1 | Output files from LDpred is placed her 2 | -------------------------------------------------------------------------------- /scripts/pgs/pgs_toolkit/Rscripts/README.md: -------------------------------------------------------------------------------- 1 | # Rscripts 2 | 3 | Misc. ``R`` scripts. -------------------------------------------------------------------------------- /sphinx-docs/source/CONTRIBUTING.md: -------------------------------------------------------------------------------- 1 | ```{include} ../../CONTRIBUTING.md 2 | ``` 3 | -------------------------------------------------------------------------------- /sphinx-docs/source/docker/README.md: -------------------------------------------------------------------------------- 1 | ```{include} ../../../docker/README.md 2 | ``` -------------------------------------------------------------------------------- /sphinx-docs/source/docs/README.md: -------------------------------------------------------------------------------- 1 | ```{include} ../../../docs/README.md 2 | ``` 3 | -------------------------------------------------------------------------------- /reference/hapmap3/.gitattributes: -------------------------------------------------------------------------------- 1 | w_hm3.justrs filter=lfs diff=lfs merge=lfs -text 2 | -------------------------------------------------------------------------------- /reference/examples/regenie/snplist_rm.txt: -------------------------------------------------------------------------------- 1 | 114 2 | 191 3 | 307 4 | 310 5 | 499 6 | 500 7 | -------------------------------------------------------------------------------- /sphinx-docs/source/docs/containers/r.md: -------------------------------------------------------------------------------- 1 | ```{include} ../../../../docs/containers/r.md 2 | ``` -------------------------------------------------------------------------------- /sphinx-docs/source/docs/singularity/r.md: -------------------------------------------------------------------------------- 1 | ```{include} ../../../../docs/containers/r.md 2 | ``` 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-------------------------------------------------------------------------------- /sphinx-docs/source/scripts/pgs/LDpred2/README.md: -------------------------------------------------------------------------------- 1 | ```{include} ../../../../../scripts/pgs/LDpred2/README.md 2 | ``` -------------------------------------------------------------------------------- /reference/examples/regenie/fid_iid_to_remove.txt: -------------------------------------------------------------------------------- 1 | 35 35 2 | 136 136 3 | 77 77 4 | 100 100 5 | 204 204 6 | 474 474 7 | -------------------------------------------------------------------------------- /sphinx-docs/source/usecases/gwas_real.md: -------------------------------------------------------------------------------- 1 | ```{include} ../../../usecases/gwas_real.md 2 | :relative-images: 3 | ``` 4 | -------------------------------------------------------------------------------- /usecases/gwas_real/dep.qq.png: 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-------------------------------------------------------------------------------- 1 | # Introduction 2 | ```{toctree} 3 | :caption: Contents 4 | ``` 5 | ```{include} ../../README.md 6 | :heading-offset: 1 7 | ``` 8 | -------------------------------------------------------------------------------- /tests/extras/ex.tar.gz: -------------------------------------------------------------------------------- 1 | version https://git-lfs.github.com/spec/v1 2 | oid sha256:a8cc31ef4906ff0b039f58502e4b80e6fa589a2926b1c3bbc5d7fe8a01957401 3 | size 1352903 4 | -------------------------------------------------------------------------------- /usecases/bolt_out/myld.log: -------------------------------------------------------------------------------- 1 | version https://git-lfs.github.com/spec/v1 2 | oid sha256:6c64d04a201277aebf8da5a75187a7c93cda721bb391f8888fe89f803492ba78 3 | size 1191 4 | -------------------------------------------------------------------------------- /usecases/gwas_demo/run1.log: 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/reference/hapgen/chr21.bed: -------------------------------------------------------------------------------- 1 | version https://git-lfs.github.com/spec/v1 2 | oid sha256:fd5487bf329127915a7c1f20ded137475d2529314284a07c0555717abf76527a 3 | size 373635003 4 | -------------------------------------------------------------------------------- /reference/hapgen/chr21.bim: -------------------------------------------------------------------------------- 1 | version https://git-lfs.github.com/spec/v1 2 | oid sha256:7e6c65beee931e538789cf6b99eb77852a9cf7a69f0bf2e1b770a16e86afe951 3 | size 5525157 4 | -------------------------------------------------------------------------------- /reference/hapgen/chr21.fam: -------------------------------------------------------------------------------- 1 | version https://git-lfs.github.com/spec/v1 2 | oid sha256:1b76f2cf150934ae50b8e08aa7030e8c2d85f4a5b37e86afa6c4547711eb66b1 3 | size 257780 4 | -------------------------------------------------------------------------------- /reference/hrc/README.md: -------------------------------------------------------------------------------- 1 | The list of sites from http://www.haplotype-reference-consortium.org/site 2 | 3 | Original README file is provied here: [README](README). 4 | 5 | -------------------------------------------------------------------------------- /usecases/gwas_demo/run1_chr1.log: -------------------------------------------------------------------------------- 1 | version https://git-lfs.github.com/spec/v1 2 | oid sha256:aa6b28d1a41e281ae152d075c7073c9595f0a54a23e33f266769d0d82d6cb0c4 3 | size 2258 4 | -------------------------------------------------------------------------------- /usecases/gwas_demo/run1_chr2.log: -------------------------------------------------------------------------------- 1 | version https://git-lfs.github.com/spec/v1 2 | oid 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https://storage.googleapis.com/broad-alkesgroup-public/LDSCORE/hapmap3_snps.tgz 3 | 4 | -------------------------------------------------------------------------------- /sphinx-docs/source/API.md: -------------------------------------------------------------------------------- 1 | # API reference 2 | ```{toctree} 3 | :caption: Contents 4 | ``` 5 | ## gwas.py 6 | 7 | ```{eval-rst} 8 | .. automodule:: gwas 9 | :members: 10 | ``` 11 | -------------------------------------------------------------------------------- /reference/examples/gctb_2.0_tutorial/about.txt: -------------------------------------------------------------------------------- 1 | downloaded from https://cnsgenomics.com/software/gctb/#Download 2 | wget https://cnsgenomics.com/software/gctb/download/gctb_2.0_tutorial.zip 3 | 4 | -------------------------------------------------------------------------------- /reference/examples/gctb_2.0_tutorial/ldm/makeldm_full.sh: 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https://git-lfs.github.com/spec/v1 2 | oid sha256:0bbee59ddd5638bef5c3dcb20002cef0a938a0e26ef82c921f986b2d9e52b152 3 | size 983 4 | -------------------------------------------------------------------------------- /reference/hrc/HRC.r1-1.GRCh37.wgs.mac5.sites.tab.gz: -------------------------------------------------------------------------------- 1 | version https://git-lfs.github.com/spec/v1 2 | oid sha256:1b45cd2a3704e04390f17f3f979527cc9b4dfbddb3d3530ceee33512abf91c30 3 | size 705582046 4 | -------------------------------------------------------------------------------- /reference/sumstats/clozuk_pgc2.meta.sumstats.txt.gz: -------------------------------------------------------------------------------- 1 | version https://git-lfs.github.com/spec/v1 2 | oid sha256:2535a277786c2558eef7462ba6fc342a7af0b4aee79dfb502f9004c6974cb4e2 3 | size 196818095 4 | -------------------------------------------------------------------------------- /sphinx-docs/source/specifications/README.md: -------------------------------------------------------------------------------- 1 | # Specifications 2 | ```{toctree} 3 | :caption: Contents 4 | geno_specification.md 5 | pheno_specification.md 6 | sumstats_specification.md 7 | ``` 8 | -------------------------------------------------------------------------------- /tests/test_LDpred2/data/tutorial_data/public-data3.bed: -------------------------------------------------------------------------------- 1 | version https://git-lfs.github.com/spec/v1 2 | oid sha256:1e775b46b22e7ad789abd5937c72e5bfe3ef727855dc1049dbc57cc5137ebe4d 3 | size 5712465 4 | -------------------------------------------------------------------------------- /tests/test_LDpred2/data/tutorial_data/public-data3.bim: -------------------------------------------------------------------------------- 1 | version https://git-lfs.github.com/spec/v1 2 | oid sha256:c90678cc03fc3bd097dfcab0d0acfd016afb422fe9e4c1c6082069dd4e89aac1 3 | size 1838622 4 | 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/reference/sumstats/SavageJansen_2018_intelligence_metaanalysis.txt.gz: -------------------------------------------------------------------------------- 1 | version https://git-lfs.github.com/spec/v1 2 | oid sha256:37c89eef6e5abe15e300596bbe998612646c8b79416ab548b8bed579768dcc26 3 | size 461082898 4 | -------------------------------------------------------------------------------- /containers/README.md: -------------------------------------------------------------------------------- 1 | # Containers 2 | 3 | Destination for built Singularity/Apptainer container files (.sif). 4 | For more details of these files, please confer [docs/containers/README](./../../docs/containers/README.md) -------------------------------------------------------------------------------- /docker/scripts/install_simu.sh: -------------------------------------------------------------------------------- 1 | #!/bin/sh 2 | set -euo pipefail 3 | 4 | wget --no-check-certificate https://github.com/precimed/simu/releases/download/v0.9.4/simu_linux 5 | chmod +x simu_linux 6 | cp simu_linux /bin/ 7 | -------------------------------------------------------------------------------- /reference/examples/gctb_2.0_tutorial/ldm/shrunk_mcpu/chr22/1000G_eur_chr22.log: -------------------------------------------------------------------------------- 1 | version https://git-lfs.github.com/spec/v1 2 | oid sha256:3a0989287efe57019741fab1871efdab12f13bcc46b7b0ecec4a7dcf90c0579e 3 | size 2872 4 | -------------------------------------------------------------------------------- /reference/examples/gctb_2.0_tutorial/ldm/shrunk_mcpu/chr22/1000G_eur_chr22.mldmlist: -------------------------------------------------------------------------------- 1 | version https://git-lfs.github.com/spec/v1 2 | oid sha256:a9a80d10cdb544182d1a3e7e85b0c07344b86c4dbc6bf5f171ab45822de5b1b9 3 | size 470 4 | -------------------------------------------------------------------------------- /reference/examples/gctb_2.0_tutorial/pheno_generation/1000G_genos_scaled.Rdata: -------------------------------------------------------------------------------- 1 | version https://git-lfs.github.com/spec/v1 2 | oid sha256:3dde7f5ad01f33aa08c060119cd217b173047d7c0685eafc85bc8743d4d68904 3 | size 2261608 4 | -------------------------------------------------------------------------------- /reference/examples/gctb_2.0_tutorial/pheno_generation/pheno_generate_validation.R: -------------------------------------------------------------------------------- 1 | version https://git-lfs.github.com/spec/v1 2 | oid sha256:e9968c0930ccc0c63a5eadd59b7abd3bb613acd2d285c25e52a6a7e8c0ddf67b 3 | size 6068 4 | -------------------------------------------------------------------------------- /sphinx-docs/source/scripts/README.md: -------------------------------------------------------------------------------- 1 | # Scripts 2 | Documentation of helper scripts provided with this project 3 | ```{toctree} 4 | :caption: Contents 5 | :maxdepth: 1 6 | gwas/README.md 7 | pgs/LDpred2/README.md 8 | ``` 9 | -------------------------------------------------------------------------------- /docker/scripts/install_ldak.sh: -------------------------------------------------------------------------------- 1 | #!/bin/sh 2 | set -euo pipefail 3 | 4 | wget https://github.com/dougspeed/LDAK/raw/4ee871be17d8ea406494211638a5ead677e7dd47/ldak6.linux 5 | chmod a+x ldak6.linux 6 | cp ldak6.linux /bin/ldak 7 | -------------------------------------------------------------------------------- /reference/examples/gctb_2.0_tutorial/ldm/shrunk/chr22/1000G_eur_chr22.ldm.shrunk.log: -------------------------------------------------------------------------------- 1 | version https://git-lfs.github.com/spec/v1 2 | oid sha256:d6c9d87fd9570ed9c5117f72d8678e817fb03fd5c82e90529ce9407d79da59cb 3 | size 440 4 | -------------------------------------------------------------------------------- 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sha256:aa7e035ac5f29775076628e6fddd71a9edaa62e970002d633900babd63ea358f 3 | size 20000 4 | -------------------------------------------------------------------------------- /reference/examples/gctb_2.0_tutorial/sbayesr/gctb_out_r_1000G_eur_sparse/sim_20.mcmcsamples.CovEffects: -------------------------------------------------------------------------------- 1 | version https://git-lfs.github.com/spec/v1 2 | oid sha256:aa7e035ac5f29775076628e6fddd71a9edaa62e970002d633900babd63ea358f 3 | size 20000 4 | -------------------------------------------------------------------------------- /usecases/pgs/README.md: -------------------------------------------------------------------------------- 1 | # PGS 2 | 3 | Polygenic score (PGS) calculations in CoMorMent 4 | 5 | ## LDpred2 6 | 7 | For indepth details of running PGS calculations using LDpred2, please refer to the corresponding [README](./../../scripts/pgs/LDpred2). 8 | -------------------------------------------------------------------------------- /reference/examples/regenie/example_3chr.pgrs.argsfile: -------------------------------------------------------------------------------- 1 | --pheno-file /REF/examples/regenie/example_3chr.pheno 2 | --geno-file /REF/examples/regenie/example_3chr.bed 3 | --geno-ld-file /REF/examples/regenie/example_3chr.bed 4 | --chr2use 1-3 5 | --variance-standardize 6 | -------------------------------------------------------------------------------- /tests/test_LDpred2/.gitignore: -------------------------------------------------------------------------------- 1 | # Store data converted from plink to bigsnpr 2 | data/ 3 | !data/README 4 | !data/individual-ids.txt 5 | !unittest/data/ 6 | # Gentic maps 7 | maps/ 8 | !maps/README 9 | output/ 10 | !output/README 11 | temp/ 12 | !temp/README 13 | -------------------------------------------------------------------------------- /scripts/gwas/README.md: -------------------------------------------------------------------------------- 1 | # GWAS 2 | 3 | For indepth explanation of the ``gwas.py`` and ``config.yaml`` codes provided here, please see the [usecases](./../../usecases/README.md): 4 | 5 | * [gwas_demo](./../../usecases/gwas_demo.md) 6 | * [gwas_real](./../../usecases/gwas_real.md) 7 | -------------------------------------------------------------------------------- /docker/scripts/stub.sh: -------------------------------------------------------------------------------- 1 | #!/bin/sh 2 | MYSELF=`which "$0" 2>/dev/null` 3 | [ $? -gt 0 -a -f "$0" ] && MYSELF="./$0" 4 | java=java 5 | if test -n "$JAVA_HOME"; then 6 | java="$JAVA_HOME/bin/java" 7 | fi 8 | java_args=-Xmx1g 9 | exec "$java" $java_args -jar $MYSELF "$@" 10 | exit 1 -------------------------------------------------------------------------------- /sphinx-docs/source/GETTING_STARTED.md: -------------------------------------------------------------------------------- 1 | # Getting started 2 | 3 | To get started using a bare-bones container setup, please confer the following pages: 4 | 5 | ```{toctree} 6 | :caption: Contents 7 | ``` 8 | ```{include} ../../docs/containers/hello.md 9 | :heading-offset: 1 10 | ``` -------------------------------------------------------------------------------- /docker/scripts/install_bedtools.sh: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | set -euo pipefail 3 | 4 | VERSION="2.31.1" 5 | wget https://github.com/arq5x/bedtools2/releases/download/v$VERSION/bedtools-$VERSION.tar.gz 6 | tar -zxvf bedtools-$VERSION.tar.gz 7 | cd bedtools2 8 | make -j4 9 | cp bin/* /bin 10 | 11 | -------------------------------------------------------------------------------- /docker/scripts/install_duohmm.sh: -------------------------------------------------------------------------------- 1 | #!/bin/sh 2 | set -euo pipefail 3 | 4 | git clone https://github.com/jaredo/duohmm.git && \ 5 | cd duohmm && \ 6 | git checkout 95bd3958792aeaa43e9f301ead139e5691d7c165 && \ 7 | make -j 4 && \ 8 | cp bin/duohmm /usr/bin/ 9 | 10 | 11 | -------------------------------------------------------------------------------- /docker/scripts/install_flashpca.sh: -------------------------------------------------------------------------------- 1 | #!/bin/sh 2 | set -euo pipefail 3 | 4 | wget --no-check-certificate https://github.com/gabraham/flashpca/releases/download/v2.0/flashpca_x86-64.gz && \ 5 | gunzip flashpca_x86-64.gz && \ 6 | chmod +x flashpca_x86-64 && \ 7 | cp flashpca_x86-64 /bin 8 | -------------------------------------------------------------------------------- /.readthedocs.yml: -------------------------------------------------------------------------------- 1 | version: 2 2 | 3 | build: 4 | os: ubuntu-22.04 5 | tools: 6 | python: "mambaforge-22.9" 7 | 8 | sphinx: 9 | configuration: sphinx-docs/source/conf.py 10 | 11 | formats: 12 | - pdf 13 | - epub 14 | 15 | conda: 16 | environment: sphinx-docs/source/environment.yml 17 | -------------------------------------------------------------------------------- /docker/scripts/install_plink2.sh: -------------------------------------------------------------------------------- 1 | #!/bin/sh 2 | set -euo pipefail 3 | 4 | wget --no-check-certificate https://github.com/chrchang/plink-ng/releases/download/v2.0.0-a.6.28/plink2_linux_x86_64.zip && \ 5 | unzip -j plink2_linux_x86_64.zip && \ 6 | rm -rf plink2_linux_x86_64.zip 7 | 8 | cp plink2 /bin 9 | -------------------------------------------------------------------------------- /docker/scripts/install_plink.sh: -------------------------------------------------------------------------------- 1 | #!/bin/sh 2 | set -euo pipefail 3 | 4 | # plink 5 | wget --no-check-certificate https://github.com/chrchang/plink-ng/releases/download/v1.9.0-b.7.11/plink_linux_x86_64.zip && \ 6 | unzip -j plink_linux_x86_64.zip && \ 7 | rm -rf plink_linux_x86_64.zip 8 | cp plink /bin 9 | -------------------------------------------------------------------------------- /docker/scripts/install_gcta.sh: -------------------------------------------------------------------------------- 1 | #!/bin/sh 2 | set -euo pipefail 3 | 4 | # gcta 5 | VERSION="1.94.1" 6 | curl -O -J -L https://github.com/jianyangqt/gcta/releases/download/v$VERSION/gcta-$VERSION-linux-x86_64-static && \ 7 | mv gcta-$VERSION-linux-x86_64-static /bin/gcta64 && \ 8 | chmod +x /bin/gcta64 9 | 10 | -------------------------------------------------------------------------------- /reference/examples/regenie/example_3chr_bgen.argsfile: -------------------------------------------------------------------------------- 1 | --pheno-file /REF/examples/regenie/example_3chr.pheno 2 | --geno-fit-file /REF/examples/regenie/example_3chr.bed 3 | --geno-file /REF/examples/regenie/example_3chr.bgen 4 | --info-file /REF/examples/regenie/example_3chr.info --info 0.8 5 | --chr2use 1-3 6 | --variance-standardize 7 | -------------------------------------------------------------------------------- /reference/examples/regenie/example_3chr_pgen.argsfile: -------------------------------------------------------------------------------- 1 | --pheno-file /REF/examples/regenie/example_3chr.pheno 2 | --geno-fit-file /REF/examples/regenie/example_3chr.bed 3 | --geno-file /REF/examples/regenie/example_3chr.pgen 4 | --info-file /REF/examples/regenie/example_3chr.info --info 0.8 5 | --chr2use 1-3 6 | --variance-standardize 7 | -------------------------------------------------------------------------------- /sphinx-docs/source/MAIN.md: -------------------------------------------------------------------------------- 1 | ```{toctree} 2 | :caption: Contents 3 | INTRODUCTION.md 4 | GETTING_STARTED.md 5 | INSTALL.md 6 | containers/README.md 7 | specifications/README.md 8 | reference/README.md 9 | scripts/README.md 10 | usecases/README.md 11 | API.md 12 | CONTRIBUTING.md 13 | CHANGELOG.md 14 | INTERNAL.md 15 | ``` 16 | -------------------------------------------------------------------------------- /docker/scripts/install_prsice.sh: -------------------------------------------------------------------------------- 1 | #!/bin/sh 2 | set -euo pipefail 3 | 4 | # Prsice 5 | wget --no-check-certificate https://github.com/choishingwan/PRSice/releases/download/2.3.5/PRSice_linux.zip && \ 6 | unzip PRSice_linux.zip && \ 7 | rm -rf PRSice_linux.zip 8 | 9 | cp PRSice_linux /bin 10 | chmod +x /bin/PRSice_linux 11 | -------------------------------------------------------------------------------- /.github/ISSUE_TEMPLATE/documentation-issue.md: -------------------------------------------------------------------------------- 1 | --- 2 | name: Documentation issue 3 | about: Suggest improvements to the documentation 4 | title: '' 5 | labels: '' 6 | assignees: '' 7 | 8 | --- 9 | 10 | ** The documentation issue** 11 | A clear and concise description of what could be improved in the documentation and/or README files. 12 | -------------------------------------------------------------------------------- /docker/scripts/install_snptest.sh: -------------------------------------------------------------------------------- 1 | #!/bin/sh 2 | set -euo pipefail 3 | 4 | # snptest 5 | wget --no-check-certificate http://www.well.ox.ac.uk/~gav/resources/snptest_v2.5.6_CentOS_Linux7.8-x86_64_dynamic.tgz 6 | tar -xvzf snptest_v2.5.6_CentOS_Linux7.8-x86_64_dynamic.tgz 7 | cp snptest_v2.5.6_CentOS_Linux7.8.2003-x86_64_dynamic/snptest_v2.5.6 /bin/snptest 8 | -------------------------------------------------------------------------------- /sphinx-docs/source/environment.yml: -------------------------------------------------------------------------------- 1 | name: sphinx 2 | channels: 3 | - conda-forge 4 | - defaults 5 | dependencies: 6 | - python=3.11 7 | - sphinx 8 | - sphinx_rtd_theme 9 | - sphinx-design 10 | - myst-parser 11 | - make 12 | - linkify-it-py 13 | - numpydoc 14 | - numpy 15 | - pandas 16 | - six 17 | - scipy 18 | - pyyaml 19 | -------------------------------------------------------------------------------- /reference/examples/regenie/example_3chr.argsfile: -------------------------------------------------------------------------------- 1 | --pheno-file /REF/examples/regenie/example_3chr.pheno 2 | --geno-fit-file /REF/examples/regenie/example_3chr.bed 3 | --geno-file /REF/examples/regenie/example_3chr.bed 4 | --info-file /REF/examples/regenie/example_3chr.info --info 0.8 5 | --chr2use 1-3 6 | --variance-standardize 7 | --maf 0.1 --geno 0.5 --hwe 0.01 8 | -------------------------------------------------------------------------------- /docker/scripts/install_metal.sh: -------------------------------------------------------------------------------- 1 | #!/bin/sh 2 | set -euo pipefail 3 | 4 | # metal 5 | wget --no-check-certificate https://github.com/statgen/METAL/archive/refs/tags/2020-05-05.tar.gz 6 | tar -xvzf 2020-05-05.tar.gz 7 | 8 | mkdir build && cd build 9 | cmake -DCMAKE_BUILD_TYPE=Release ../METAL-2020-05-05/. 10 | make -j4 11 | make install 12 | cp bin/metal /bin 13 | -------------------------------------------------------------------------------- /docker/scripts/install_vcftools.sh: -------------------------------------------------------------------------------- 1 | #!/bin/sh 2 | set -euo pipefail 3 | 4 | # vcfools 5 | git clone https://github.com/vcftools/vcftools.git && \ 6 | cd vcftools && \ 7 | git reset --hard d511f469e87c2ac9779bcdc3670b2b51667935fe && \ 8 | ./autogen.sh && \ 9 | ./configure && \ 10 | make -j6 && \ 11 | make install 12 | 13 | 14 | #cp vcftools /bin 15 | -------------------------------------------------------------------------------- /reference/examples/regenie/example_3chr.pheno.dict: -------------------------------------------------------------------------------- 1 | COLUMN,TYPE,DESCRIPTION 2 | IID,IID,Identifier 3 | PHENO,CONTINUOUS,phenotype 4 | PHENO2,CONTINUOUS,second phenotype 5 | CASE,BINARY,case/control phenotype 6 | CASE2,BINARY,another case/control phenotype 7 | PC1,CONTINUOUS,principal component1 8 | PC2,CONTINUOUS,second principal component 9 | BATCH,NOMINAL,genotype batch 10 | -------------------------------------------------------------------------------- /docker/scripts/install_miniforge.sh: -------------------------------------------------------------------------------- 1 | #!/bin/sh 2 | set -euo pipefail 3 | 4 | version=25.11.0-1 5 | curl -sSL https://github.com/conda-forge/miniforge/releases/download/$version/Miniforge3-$version-$(uname)-$(uname -m).sh -o /tmp/miniforge.sh 6 | mkdir /root/.conda 7 | bash /tmp/miniforge.sh -bfp /usr/local 8 | rm -rf /tmp/miniforge.sh 9 | 10 | export PATH=$PATH:/opt/conda/bin 11 | -------------------------------------------------------------------------------- /docker/scripts/install_gctb.sh: -------------------------------------------------------------------------------- 1 | #!/bin/sh 2 | set -euo pipefail 3 | 4 | # gctb 5 | VERSION="2.04.3" 6 | wget --no-check-certificate https://cnsgenomics.com/software/gctb/download/gctb_${VERSION}_Linux.zip && \ 7 | unzip gctb_${VERSION}_Linux.zip && \ 8 | rm -rf gctb_${VERSION}_Linux.zip 9 | 10 | mv gctb_${VERSION}_Linux/* . 11 | cp gctb /bin 12 | 13 | chmod 755 /bin/gctb 14 | -------------------------------------------------------------------------------- /reference/examples/regenie/example_3chr_vcf.argsfile: -------------------------------------------------------------------------------- 1 | --pheno-file /REF/examples/regenie/example_3chr.pheno 2 | --geno-fit-file /REF/examples/regenie/example_3chr.bed 3 | --geno-file /REF/examples/regenie/example_3chr.vcf.gz 4 | --info-file /REF/examples/regenie/example_3chr.info --info 0.8 5 | --chr2use 1-3 6 | --variance-standardize 7 | --maf 0.1 --geno 0.5 --hwe 0.01 8 | --vcf-field GT 9 | 10 | -------------------------------------------------------------------------------- /sphinx-docs/source/containers/README.md: -------------------------------------------------------------------------------- 1 | # Containers 2 | ```{toctree} 3 | :caption: Contents 4 | ``` 5 | ```{include} ../../../docs/containers/gwas.md 6 | :heading-offset: 1 7 | ``` 8 | ```{include} ../../../docs/containers/python3.md 9 | :heading-offset: 1 10 | ``` 11 | ```{include} ../../../docs/containers/r.md 12 | :heading-offset: 1 13 | ``` 14 | ```{include} external.md 15 | :heading-offset: 1 16 | ``` 17 | -------------------------------------------------------------------------------- /scripts/pgs/README.md: -------------------------------------------------------------------------------- 1 | # PGS 2 | 3 | Polygenic Score calculations and evaluations 4 | 5 | ## LDpred2 6 | 7 | Polygenic score (PGS) codes are provided in [LDpred2](./LDpred2/README.md). 8 | 9 | ## PGS toolkit 10 | 11 | PGS toolkit is a collection of scripts to calculate PGS and evaluate PGS performance. The scripts are written in Python 3.6+ and R 3.6+. 12 | See [PGS toolkit](./pgs_toolkit/README.md) for details. 13 | -------------------------------------------------------------------------------- /scripts/pgs/pgs_toolkit/Rscripts/update_effect_size.R: -------------------------------------------------------------------------------- 1 | library(argparser, quietly=T) 2 | library(data.table) 3 | 4 | # capture command-line input 5 | par <- arg_parser('') 6 | par <- add_argument(par, "qcfile", help=".gz input file") 7 | par <- add_argument(par, "transformed", help=".transformed output file") 8 | parsed <- parse_args(par) 9 | 10 | dat <- fread(parsed$qcfile) 11 | fwrite(dat[,BETA:=log(OR)], parsed$transformed, sep="\t") 12 | -------------------------------------------------------------------------------- /usecases/gwas_real/moba.bgen.argsfile: -------------------------------------------------------------------------------- 1 | --pheno-file moba.pheno 2 | --geno-fit-file moba.hm3.withoutFID.bed 3 | --geno-file /cluster/projects/p697/genotype/MoBa_98k_post-imputationQC/bgen/chr@_MERGED.bgen 4 | --fam moba.hm3.withoutFID.fam 5 | --singularity-bind "$COMORMENT/containers/reference:/REF:ro,/cluster/projects/p697:/cluster/projects/p697" 6 | --covar PC1 PC2 PC3 PC4 PC5 PC6 PC7 PC8 PC9 PC10 genotyping_batch YOB Sex 7 | --variance-standardize 8 | -------------------------------------------------------------------------------- /docker/scripts/install_bgenix.sh: -------------------------------------------------------------------------------- 1 | #!/bin/sh 2 | set -euo pipefail 3 | 4 | # build bgen 5 | # fixed build issue in https://enkre.net/cgi-bin/code/bgen/tktview/52cb8e5b67. 6 | # Use the same git SHA in the install_regenie.sh script 7 | SHA="4f70490b4c54be43714900636b514d2b882544df" 8 | git clone https://github.com/dbolser/bgen.git && \ 9 | cd bgen && git checkout $SHA && \ 10 | ./waf configure --prefix=/usr && \ 11 | ./waf install 12 | -------------------------------------------------------------------------------- /sphinx-docs/source/reference/opensnp.md: -------------------------------------------------------------------------------- 1 | # openSNP example data 2 | 3 | This project relies on data from [openSNP](https://opensnp.org/), a platform for sharing personal genomics data. This public data is licensed under the [CC0](https://creativecommons.org/public-domain/cc0/). 4 | 5 | To obtain the datas for use in various examples provided here, see detailed instructions at [https://github.com/comorment/opensnp](https://github.com/comorment/opensnp). 6 | -------------------------------------------------------------------------------- /docker/scripts/install_plink2_avx2.sh: -------------------------------------------------------------------------------- 1 | #!/bin/sh 2 | set -euo pipefail 3 | 4 | wget --no-check-certificate https://github.com/chrchang/plink-ng/releases/download/v2.0.0-a.6.28/plink2_linux_avx2.zip && \ 5 | unzip -j plink2_linux_avx2.zip && \ 6 | rm -rf plink2_linux_avx2.zip 7 | # we install non-avx plink2 so that default plink runs on any CPU architecture 8 | 9 | 10 | mv plink2 plink2_avx2 11 | rm -f plink2 12 | 13 | cp plink2_avx2 /bin 14 | -------------------------------------------------------------------------------- /.github/workflows/greetings.yml: -------------------------------------------------------------------------------- 1 | name: Greetings 2 | 3 | on: [pull_request, issues] 4 | 5 | jobs: 6 | greeting: 7 | runs-on: ubuntu-latest 8 | steps: 9 | - uses: actions/first-interaction@v1 10 | with: 11 | repo-token: ${{ secrets.GITHUB_TOKEN }} 12 | issue-message: 'Hello @${{ github.actor }} , thank you for submitting an issue!' 13 | pr-message: 'Hello @${{ github.actor }} , thank you submitting a pull request!' -------------------------------------------------------------------------------- /usecases/gwas_real/moba.bed.argsfile: -------------------------------------------------------------------------------- 1 | --pheno-file moba.pheno 2 | --geno-fit-file moba.hm3.withoutFID.bed 3 | --geno-file /cluster/projects/p697/genotype/MoBa_98k_post-imputationQC/98k-ec-eur-fin-batch-basic-qc-withoutFID.bed 4 | --fam moba.hm3.withoutFID.fam 5 | --singularity-bind "$COMORMENT/containers/reference:/REF:ro,/cluster/projects/p697:/cluster/projects/p697" 6 | --covar PC1 PC2 PC3 PC4 PC5 PC6 PC7 PC8 PC9 PC10 genotyping_batch YOB Sex 7 | --variance-standardize 8 | -------------------------------------------------------------------------------- /.github/workflows/docker.yml: -------------------------------------------------------------------------------- 1 | name: Dockerfile Linter 2 | 3 | on: [push, pull_request] 4 | 5 | jobs: 6 | hadolint: 7 | name: runner / hadolint 8 | runs-on: ubuntu-latest 9 | steps: 10 | - name: Check out code 11 | uses: actions/checkout@v3 12 | - name: hadolint 13 | uses: reviewdog/action-hadolint@v1 14 | with: 15 | reporter: github-pr-review # Default is github-pr-check 16 | fail_on_error: true 17 | -------------------------------------------------------------------------------- /version/version.py: -------------------------------------------------------------------------------- 1 | _MAJOR = "1" 2 | _MINOR = "14" 3 | # On main and in a nightly release the patch should be one ahead of the last 4 | # released build. 5 | _PATCH = "0" 6 | # This is mainly for nightly builds which have the suffix ".dev$DATE". See 7 | # https://semver.org/#is-v123-a-semantic-version for the semantics. 8 | _SUFFIX = "" 9 | 10 | VERSION_SHORT = "{0}.{1}".format(_MAJOR, _MINOR) 11 | VERSION = "{0}.{1}.{2}{3}".format(_MAJOR, _MINOR, _PATCH, _SUFFIX) 12 | -------------------------------------------------------------------------------- /docker/scripts/install_eagle.sh: -------------------------------------------------------------------------------- 1 | #!/bin/sh 2 | set -euo pipefail 3 | 4 | apt-get update && apt-get install --no-install-recommends \ 5 | libopenblas-dev=0.3.26+ds-1 \ 6 | -y && \ 7 | apt-get clean && \ 8 | rm -rf /var/lib/apt/lists/* 9 | 10 | git clone --depth 1 -b v2.4.1 https://github.com/poruloh/Eagle.git && \ 11 | cd Eagle && \ 12 | git apply ../eagle.diff && \ 13 | cd src && \ 14 | make -j 4 && \ 15 | cp eagle /usr/bin/ 16 | 17 | 18 | -------------------------------------------------------------------------------- /docker/dockerfiles/hello/Dockerfile: -------------------------------------------------------------------------------- 1 | # demo container 2 | FROM ubuntu:24.04 3 | 4 | ENV TZ=Europe 5 | ENV DEBIAN_FRONTEND=noninteractive 6 | 7 | # Essential Tools 8 | WORKDIR /tmp 9 | COPY /scripts/apt_get_essential.sh . 10 | RUN bash apt_get_essential.sh && \ 11 | rm apt_get_essential.sh 12 | 13 | # Plink 14 | WORKDIR /tmp/plink 15 | COPY /scripts/install_plink.sh /tmp/plink/ 16 | RUN bash /tmp/plink/install_plink.sh && \ 17 | rm -rf /tmp/plink 18 | 19 | WORKDIR /tools 20 | -------------------------------------------------------------------------------- /docker/scripts/install_beagle.sh: -------------------------------------------------------------------------------- 1 | #!/bin/sh 2 | set -euo pipefail 3 | 4 | # additional deps 5 | apt-get update && apt-get install --no-install-recommends \ 6 | default-jre=2:1.21-75+exp1 \ 7 | -y && \ 8 | apt-get clean && \ 9 | rm -rf /var/lib/apt/lists/* 10 | 11 | wget http://faculty.washington.edu/browning/beagle/beagle.22Jul22.46e.jar && \ 12 | mv beagle.22Jul22.46e.jar beagle.jar 13 | 14 | cat stub.sh beagle.jar > /usr/bin/beagle && chmod +x /usr/bin/beagle 15 | -------------------------------------------------------------------------------- /docker/scripts/install_king.sh: -------------------------------------------------------------------------------- 1 | #!/bin/sh 2 | set -euo pipefail 3 | 4 | # king 5 | VERSION="232" 6 | wget --debug --no-check-certificate --user-agent="Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Ubuntu Chromium/83.0.4103.61 Chrome/83.0.4103.61 Safari/537.36" https://www.kingrelatedness.com/executables/Linux-king$VERSION.tar.gz && \ 7 | tar -xvzf Linux-king$VERSION.tar.gz && \ 8 | rm -rf Linux-king$VERSION.tar.gz 9 | 10 | cp king /bin 11 | 12 | rm -rf * -------------------------------------------------------------------------------- /docker/scripts/patches/shapeit4.makefile.diff: -------------------------------------------------------------------------------- 1 | diff --git a/makefile b/makefile 2 | index 7a5cbd8..ef8e537 100644 3 | --- a/makefile 4 | +++ b/makefile 5 | @@ -2,8 +2,8 @@ 6 | CXX=g++ -std=c++11 7 | 8 | #HTSLIB LIBRARY [SPECIFY YOUR OWN PATHS] 9 | -HTSLIB_INC=$(HOME)/Tools/htslib-1.11 10 | -HTSLIB_LIB=$(HOME)/Tools/htslib-1.11/libhts.a 11 | +HTSLIB_INC=/usr/include 12 | +HTSLIB_LIB=/usr/lib/libhts.a 13 | 14 | #BOOST IOSTREAM & PROGRAM_OPTION LIBRARIES [SPECIFY YOUR OWN PATHS] 15 | BOOST_INC=/usr/include 16 | -------------------------------------------------------------------------------- /docker/scripts/install_shapeit4.sh: -------------------------------------------------------------------------------- 1 | #!/bin/sh 2 | set -euo pipefail 3 | 4 | # additional deps 5 | apt-get update && apt-get install --no-install-recommends \ 6 | libboost-program-options-dev=1.83.0.1ubuntu2 \ 7 | -y && \ 8 | apt-get clean && \ 9 | rm -rf /var/lib/apt/lists/* 10 | 11 | # build shapeit4 12 | git clone --depth 1 -b v4.2.2 https://github.com/odelaneau/shapeit4.git && \ 13 | cd shapeit4 && \ 14 | patch makefile < ../shapeit4.makefile.diff 15 | make -j 4 && \ 16 | cp bin/* /usr/bin/. -------------------------------------------------------------------------------- /docker/scripts/install_samtools.sh: -------------------------------------------------------------------------------- 1 | #!/bin/sh 2 | set -euo pipefail 3 | 4 | apt-get update && apt-get install -y --no-install-recommends \ 5 | libncurses-dev=6.4+20240113-1ubuntu2 \ 6 | && \ 7 | apt-get clean && \ 8 | rm -rf /var/lib/apt/lists/* 9 | 10 | # samtools 11 | git clone --depth 1 -b 1.19.2 https://github.com/samtools/samtools.git && \ 12 | cd samtools && \ 13 | autoheader && \ 14 | autoconf -Wno-syntax && \ 15 | ./configure --with-htslib=/usr/ && \ 16 | make -j12 && \ 17 | make install 18 | -------------------------------------------------------------------------------- /reference/examples/gwama/pop1.txt: -------------------------------------------------------------------------------- 1 | MARKERNAME STRAND IMPUTED EA NEA BETA SE 2 | rs12565286 + 0 G C -0.0223417 0.403115 3 | rs2977670 + 0 C G -0.0137211 0.406126 4 | rs12138618 + 0 G A -0.0763812 0.3712373 5 | rs3094315 + 0 G A 0.0258089 0.101264 6 | rs3131968 + 0 G A -0.3734 0.1012374 7 | rs2519016 + 1 T C 0.26655 0.347234 8 | rs12562034 + 1 G A 0.00923484 0.279129 9 | rs2905035 + 1 G A -0.0435863 NA 10 | rs12124819 + 1 A G 0.0262434 0.121293 11 | rs2980319 + 1 T A -0.0423165 0.1241691 12 | rs4040617 + 1 A G 0.0230683 0.1012426 13 | --------------------------------------------------------------------------------