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| # ukb_exomes | ||
| # ukb_exomes | ||
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| The results of this analysis are released in Google Cloud bucket `gs://ukbb-exome-public/`: | ||
| - Main summary statistics MatrixTable: | ||
| + Variant-level results: `gs://ukbb-exome-public/500k/results/variant_results.mt` | ||
| + Gene-level results: `gs://ukbb-exome-public/500k/results/results.mt` | ||
| - QC information annotated MatrixTable or Hail Table: | ||
| + Variant-level: `gs://ukbb-exome-public/500k/qc/variant_qc_metrics_ukb_exomes_500k{.mt, .ht}` | ||
| + Gene-level: `gs://ukbb-exome-public/500k/qc/gene_qc_metrics_ukb_exomes_500k{.mt, .ht}` | ||
| + Phenotype: `gs://ukbb-exome-public/500k/qc/pheno_qc_metrics_ukb_exomes_500k.ht` | ||
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| We also provide the following derived datasets for convenience: | ||
| - Gene-annotation group cumulative allele frequency table: `gs://ukbb-exome-public/500k/qc/gene_caf_500k.ht` | ||
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| These files can be accessed by cloning this and the https://github.com/broadinstitute/ukbb_qc repo, import the `ukbb_common` python module and accessing them programmatically. We recommend using these functions, as they apply our QC metrics and include convenience metrics such as lambda GC. | ||
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| ``` | ||
| %%bash | ||
| git clone https://github.com/broadinstitute/ukbb_qc | ||
| git clone https://github.com/Nealelab/ukb_exomes | ||
| ``` | ||
|
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||
| ``` | ||
| from ukb_exomes import * | ||
| from ukbb_common import * | ||
| ``` | ||
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| To read the original MatrixTables with 4529 phenotypes: | ||
| ``` | ||
| ## Gene-level results | ||
| gene_mt = hl.read_matrix_table(get_results_mt_path(result_type='gene')) | ||
| ## Variant-level results | ||
| var_mt = hl.read_matrix_table(get_results_mt_path(result_type='variant')) | ||
| ``` | ||
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| To read the full MatrixTables with QC information annotated: | ||
| ``` | ||
| ## Gene-level results | ||
| gene_mt = hl.read_matrix_table(load_final_sumstats_table(result_type='gene', extension="mt")) | ||
| ## Variant-level results | ||
| var_mt = hl.read_matrix_table(load_final_sumstats_table(result_type='variant', extension="mt")) | ||
| ``` | ||
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| To get the final QCed MatrixTables (Note that we have two options for `test_type`: `skato` and `burden`, which indicates which test the lambda GC used here were computed from): | ||
| ``` | ||
| ## Gene-level results | ||
| gene_mt = get_qc_result_mt(result_type="gene", test_type="skato") | ||
| ## Variant-level results | ||
| var_mt = get_qc_result_mt(result_type="variant", test_type="skato") | ||
| ``` | ||
|
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| The basic summary statistics of the gene-based tests have the following schema: | ||
| ``` | ||
| ---------------------------------------- | ||
| Global fields: | ||
| 'coverage_min': int32 | ||
| 'expected_AC_min': int32 | ||
| 'n_var_min': int32 | ||
| 'gene_syn_lambda_min': float64 | ||
| 'pheno_lambda_min': float64 | ||
| ---------------------------------------- | ||
| Column fields: | ||
| 'n_cases': int32 | ||
| 'n_controls': int32 | ||
| 'heritability': float64 | ||
| 'saige_version': str | ||
| 'inv_normalized': str | ||
| 'trait_type': str | ||
| 'phenocode': str | ||
| 'pheno_sex': str | ||
| 'coding': str | ||
| 'modifier': str | ||
| 'n_cases_defined': int64 | ||
| 'n_cases_both_sexes': int64 | ||
| 'n_cases_females': int64 | ||
| 'n_cases_males': int64 | ||
| 'description': str | ||
| 'description_more': str | ||
| 'coding_description': str | ||
| 'category': str | ||
| 'expected_ac_col_filter': int64 | ||
| 'lambda_gc_skat': float64 | ||
| 'lambda_gc_burden': float64 | ||
| 'lambda_gc_skato': float64 | ||
| 'keep_pheno_skato': bool | ||
| 'keep_pheno_skat': bool | ||
| 'keep_pheno_burden': bool | ||
| 'keep_pheno_unrelated': bool | ||
| ---------------------------------------- | ||
| Row fields: | ||
| 'gene_id': str | ||
| 'gene_symbol': str | ||
| 'annotation': str | ||
| 'interval': interval<locus<GRCh38>> | ||
| 'markerIDs': str | ||
| 'markerAFs': str | ||
| 'total_variants': int32 | ||
| 'Nmarker_MACCate_1': int32 | ||
| 'Nmarker_MACCate_2': int32 | ||
| 'Nmarker_MACCate_3': int32 | ||
| 'Nmarker_MACCate_4': int32 | ||
| 'Nmarker_MACCate_5': int32 | ||
| 'Nmarker_MACCate_6': int32 | ||
| 'Nmarker_MACCate_7': int32 | ||
| 'Nmarker_MACCate_8': int32 | ||
| 'CAF': float64 | ||
| 'mean_coverage': float64 | ||
| 'expected_ac_row_filter': int64 | ||
| 'continuous_lambda_gc_skato': float64 | ||
| 'continuous_lambda_gc_skat': float64 | ||
| 'continuous_lambda_gc_burden': float64 | ||
| 'categorical_lambda_gc_skato': float64 | ||
| 'categorical_lambda_gc_skat': float64 | ||
| 'categorical_lambda_gc_burden': float64 | ||
| 'icd10_lambda_gc_skato': float64 | ||
| 'icd10_lambda_gc_skat': float64 | ||
| 'icd10_lambda_gc_burden': float64 | ||
| 'annotation_lambda_gc_skato': float64 | ||
| 'annotation_lambda_gc_skat': float64 | ||
| 'annotation_lambda_gc_burden': float64 | ||
| 'synonymous_lambda_gc_skato': float64 | ||
| 'synonymous_lambda_gc_skat': float64 | ||
| 'synonymous_lambda_gc_burden': float64 | ||
| 'keep_gene_skato': bool | ||
| 'keep_gene_skat': bool | ||
| 'keep_gene_burden': bool | ||
| 'keep_gene_coverage': bool | ||
| 'keep_gene_expected_ac': bool | ||
| 'keep_gene_n_var': bool | ||
| ---------------------------------------- | ||
| Entry fields: | ||
| 'Pvalue': float64 | ||
| 'Pvalue_Burden': float64 | ||
| 'Pvalue_SKAT': float64 | ||
| 'BETA_Burden': float64 | ||
| 'SE_Burden': float64 | ||
| 'Pvalue.NA': float64 | ||
| 'Pvalue_Burden.NA': float64 | ||
| 'Pvalue_SKAT.NA': float64 | ||
| 'BETA_Burden.NA': float64 | ||
| 'SE_Burden.NA': float64 | ||
| 'total_variants_pheno': int32 | ||
| 'expected_AC': float64 | ||
| 'keep_entry_expected_ac': bool | ||
| ---------------------------------------- | ||
| Column key: ['trait_type', 'phenocode', 'pheno_sex', 'coding', 'modifier'] | ||
| Row key: ['gene_id', 'gene_symbol', 'annotation'] | ||
| ---------------------------------------- | ||
| ``` | ||
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| The basic summary statistics of the variant-level tests have the following schema: | ||
| ``` | ||
| ---------------------------------------- | ||
| Global fields: | ||
| 'expected_AC_min': int32 | ||
| 'pheno_lambda_min': float64 | ||
| ---------------------------------------- | ||
| Column fields: | ||
| 'n_cases': int32 | ||
| 'n_controls': int32 | ||
| 'heritability': float64 | ||
| 'saige_version': str | ||
| 'inv_normalized': str | ||
| 'trait_type': str | ||
| 'phenocode': str | ||
| 'pheno_sex': str | ||
| 'coding': str | ||
| 'modifier': str | ||
| 'n_cases_defined': int64 | ||
| 'n_cases_both_sexes': int64 | ||
| 'n_cases_females': int64 | ||
| 'n_cases_males': int64 | ||
| 'description': str | ||
| 'description_more': str | ||
| 'coding_description': str | ||
| 'category': str | ||
| 'expected_ac_col_filter': int64 | ||
| 'lambda_gc_skat': float64 | ||
| 'lambda_gc_burden': float64 | ||
| 'lambda_gc_skato': float64 | ||
| 'keep_pheno_skato': bool | ||
| 'keep_pheno_skat': bool | ||
| 'keep_pheno_burden': bool | ||
| 'keep_pheno_unrelated': bool | ||
| ---------------------------------------- | ||
| Row fields: | ||
| 'locus': locus<GRCh38> | ||
| 'alleles': array<str> | ||
| 'markerID': str | ||
| 'gene': str | ||
| 'annotation': str | ||
| 'call_stats': struct { | ||
| AC: int32, | ||
| AF: float64, | ||
| AN: int32, | ||
| homozygote_count: int32 | ||
| } | ||
| 'expected_ac_row_filter': int64 | ||
| 'keep_var_expected_ac': bool | ||
| 'keep_var_annt': bool | ||
| ---------------------------------------- | ||
| Entry fields: | ||
| 'AC': int32 | ||
| 'AF': float64 | ||
| 'BETA': float64 | ||
| 'SE': float64 | ||
| 'AF.Cases': float64 | ||
| 'AF.Controls': float64 | ||
| 'Pvalue': float64 | ||
| 'expected_AC': float64 | ||
| 'keep_entry_expected_ac': bool | ||
| ---------------------------------------- | ||
| Column key: ['trait_type', 'phenocode', 'pheno_sex', 'coding', 'modifier'] | ||
| Row key: ['locus', 'alleles'] | ||
| ---------------------------------------- | ||
| ``` |