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00.load_sample_qc_kt.py
00.load_sample_qc_kt.py
 
 
01.load_genotype_snp_qc_kt.py
01.load_genotype_snp_qc_kt.py
 
 
02.export_vcf.py
02.export_vcf.py
 
 
03.load_genotype_vds.py
03.load_genotype_vds.py
 
 
04.subset_samples.py
04.subset_samples.py
 
 
05.create_pca_vds.py
05.create_pca_vds.py
 
 
06.run_pca.py
06.run_pca.py
 
 
07.vep_imputed_v3_sites.py
07.vep_imputed_v3_sites.py
 
 
08.categorize_vep_consequences.py
08.categorize_vep_consequences.py
 
 
09.load_mfi_vds.py
09.load_mfi_vds.py
 
 
10.run_variant_qc_autosomes.py
10.run_variant_qc_autosomes.py
 
 
11.run_variant_qc_chrX.py
11.run_variant_qc_chrX.py
 
 
12.subset_variants_autosomes.py
12.subset_variants_autosomes.py
 
 
13.subset_variants_chrX.py
13.subset_variants_chrX.py
 
 
14.create_covariates_kt.py
14.create_covariates_kt.py
 
 
15.create_phesant_pipelines.py
15.create_phesant_pipelines.py
 
 
16.create_icd10_pipelines.py
16.create_icd10_pipelines.py
 
 
17.create_finngen_pipelines.py
17.create_finngen_pipelines.py
 
 
18.create_curated_pipeline.py
18.create_curated_pipeline.py
 
 
19.create_icd10_phenotype_summaries.py
19.create_icd10_phenotype_summaries.py
 
 
20.create_finngen_phenotype_summaries.py
20.create_finngen_phenotype_summaries.py
 
 
21.create_curated_phenotype_summaries.py
21.create_curated_phenotype_summaries.py
 
 
22.run_regressions.py
22.run_regressions.py
 
 
23.export_results.py
23.export_results.py
 
 
24.create_variant_annotation_file.py
24.create_variant_annotation_file.py
 
 
25.create_phenotype_annotation_files.py
25.create_phenotype_annotation_files.py
 
 
26.create_ldsc_hm3_keytable.py
26.create_ldsc_hm3_keytable.py
 
 
27.export_ldsc_sumstats.py
27.export_ldsc_sumstats.py
 
 
README.md
README.md
 
 

README.md

UKB GWAS pipeline scripts written for Hail 0.1

DISCLAIMER: As the pipeline has migrated to Hail 0.2, these scripts are no longer used. For collaborators who have access to the google bucket used for these analyses, many of the filepaths and files (especially those in .vds format) referenced here are no longer accesible or have been deleted.