gwaslab 3.6.5__py3-none-any.whl → 3.6.7__py3-none-any.whl

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Files changed (110) hide show
  1. gwaslab/__init__.py +57 -47
  2. gwaslab/{bd_common_data.py → bd/bd_common_data.py} +10 -9
  3. gwaslab/bd/bd_config.py +28 -0
  4. gwaslab/{bd_download.py → bd/bd_download.py} +1 -1
  5. gwaslab/{bd_get_hapmap3.py → bd/bd_get_hapmap3.py} +9 -6
  6. gwaslab/bd/bd_path_manager.py +110 -0
  7. gwaslab/data/formatbook.json +805 -9
  8. gwaslab/{ldsc_irwls.py → extension/ldsc/ldsc_irwls.py} +1 -1
  9. gwaslab/{ldsc_regressions.py → extension/ldsc/ldsc_regressions.py} +2 -2
  10. gwaslab/{ldsc_sumstats.py → extension/ldsc/ldsc_sumstats.py} +2 -2
  11. gwaslab/{prscs_mcmc_gtb.py → extension/prscs/prscs_mcmc_gtb.py} +1 -1
  12. gwaslab/g_Sumstats.py +130 -96
  13. gwaslab/g_SumstatsMulti.py +69 -40
  14. gwaslab/g_SumstatsPair.py +54 -37
  15. gwaslab/g_SumstatsSet.py +88 -81
  16. gwaslab/g_SumstatsT.py +6 -6
  17. gwaslab/g_Sumstats_polars.py +84 -84
  18. gwaslab/g_meta_update.py +1 -1
  19. gwaslab/g_vchange_status.py +4 -4
  20. gwaslab/g_version.py +2 -2
  21. gwaslab/{hm_casting.py → hm/hm_casting.py} +4 -4
  22. gwaslab/{hm_casting_polars.py → hm/hm_casting_polars.py} +4 -4
  23. gwaslab/hm/hm_harmonize_sumstats.py +1635 -0
  24. gwaslab/hm_harmonize_sumstats.py +3 -8
  25. gwaslab/{io_load_ld.py → io/io_load_ld.py} +16 -13
  26. gwaslab/{io_preformat_input.py → io/io_preformat_input.py} +152 -73
  27. gwaslab/{io_preformat_input_polars.py → io/io_preformat_input_polars.py} +7 -7
  28. gwaslab/{io_read_pipcs.py → io/io_read_pipcs.py} +6 -5
  29. gwaslab/{io_read_tabular.py → io/io_read_tabular.py} +2 -2
  30. gwaslab/{io_to_formats.py → io/io_to_formats.py} +13 -9
  31. gwaslab/{io_to_pickle.py → io/io_to_pickle.py} +16 -1
  32. gwaslab/{qc_check_datatype_polars.py → qc/qc_check_datatype_polars.py} +2 -2
  33. gwaslab/{qc_fix_sumstats.py → qc/qc_fix_sumstats.py} +60 -33
  34. gwaslab/{qc_fix_sumstats_polars.py → qc/qc_fix_sumstats_polars.py} +15 -11
  35. gwaslab/{util_abf_finemapping.py → util/util_abf_finemapping.py} +2 -2
  36. gwaslab/{util_ex_calculate_ldmatrix.py → util/util_ex_calculate_ldmatrix.py} +18 -8
  37. gwaslab/{util_ex_calculate_prs.py → util/util_ex_calculate_prs.py} +2 -2
  38. gwaslab/{util_ex_ldproxyfinder.py → util/util_ex_ldproxyfinder.py} +6 -6
  39. gwaslab/{util_ex_ldsc.py → util/util_ex_ldsc.py} +18 -13
  40. gwaslab/{util_ex_match_ldmatrix.py → util/util_ex_match_ldmatrix.py} +8 -7
  41. gwaslab/util/util_ex_phewwas.py +117 -0
  42. gwaslab/{util_ex_process_h5.py → util/util_ex_process_h5.py} +2 -2
  43. gwaslab/{util_ex_process_ref.py → util/util_ex_process_ref.py} +2 -2
  44. gwaslab/{util_ex_run_2samplemr.py → util/util_ex_run_2samplemr.py} +18 -7
  45. gwaslab/{util_ex_run_ccgwas.py → util/util_ex_run_ccgwas.py} +4 -4
  46. gwaslab/{util_ex_run_clumping.py → util/util_ex_run_clumping.py} +28 -13
  47. gwaslab/{util_ex_run_coloc.py → util/util_ex_run_coloc.py} +22 -10
  48. gwaslab/{util_ex_run_hyprcoloc.py → util/util_ex_run_hyprcoloc.py} +4 -4
  49. gwaslab/{util_ex_run_magma.py → util/util_ex_run_magma.py} +21 -11
  50. gwaslab/{util_ex_run_mesusie.py → util/util_ex_run_mesusie.py} +3 -3
  51. gwaslab/{util_ex_run_mtag.py → util/util_ex_run_mtag.py} +50 -18
  52. gwaslab/{util_ex_run_prscs.py → util/util_ex_run_prscs.py} +3 -3
  53. gwaslab/{util_ex_run_scdrs.py → util/util_ex_run_scdrs.py} +10 -4
  54. gwaslab/{util_ex_run_susie.py → util/util_ex_run_susie.py} +49 -26
  55. gwaslab/{util_in_fill_data.py → util/util_in_fill_data.py} +1 -1
  56. gwaslab/{util_in_filter_value.py → util/util_in_filter_value.py} +18 -11
  57. gwaslab/{util_in_get_sig.py → util/util_in_get_sig.py} +15 -13
  58. gwaslab/{util_in_meta.py → util/util_in_meta.py} +1 -1
  59. gwaslab/{util_in_meta_polars.py → util/util_in_meta_polars.py} +1 -1
  60. gwaslab/{viz_aux_annotate_plot.py → viz/viz_aux_annotate_plot.py} +1 -1
  61. gwaslab/{viz_aux_quickfix.py → viz/viz_aux_quickfix.py} +2 -2
  62. gwaslab/{viz_plot_compare_af.py → viz/viz_plot_compare_af.py} +1 -1
  63. gwaslab/{viz_plot_compare_effect.py → viz/viz_plot_compare_effect.py} +16 -8
  64. gwaslab/{viz_plot_credible_sets.py → viz/viz_plot_credible_sets.py} +6 -6
  65. gwaslab/{viz_plot_effect.py → viz/viz_plot_effect.py} +37 -69
  66. gwaslab/{viz_plot_miamiplot.py → viz/viz_plot_miamiplot.py} +28 -20
  67. gwaslab/{viz_plot_miamiplot2.py → viz/viz_plot_miamiplot2.py} +27 -22
  68. gwaslab/{viz_plot_mqqplot.py → viz/viz_plot_mqqplot.py} +48 -38
  69. gwaslab/{viz_plot_phe_heatmap.py → viz/viz_plot_phe_heatmap.py} +18 -15
  70. gwaslab/{viz_plot_qqplot.py → viz/viz_plot_qqplot.py} +4 -2
  71. gwaslab/{viz_plot_regional2.py → viz/viz_plot_regional2.py} +11 -9
  72. gwaslab/{viz_plot_regionalplot.py → viz/viz_plot_regionalplot.py} +5 -4
  73. gwaslab/{viz_plot_rg_heatmap.py → viz/viz_plot_rg_heatmap.py} +1 -1
  74. gwaslab/{viz_plot_scatter_with_reg.py → viz/viz_plot_scatter_with_reg.py} +10 -7
  75. gwaslab/{viz_plot_stackedregional.py → viz/viz_plot_stackedregional.py} +67 -33
  76. gwaslab/{viz_plot_trumpetplot.py → viz/viz_plot_trumpetplot.py} +11 -9
  77. {gwaslab-3.6.5.dist-info → gwaslab-3.6.7.dist-info}/METADATA +1 -1
  78. gwaslab-3.6.7.dist-info/RECORD +123 -0
  79. gwaslab/bd_config.py +0 -18
  80. gwaslab-3.6.5.dist-info/RECORD +0 -120
  81. /gwaslab/{ldsc_jackknife.py → extension/ldsc/ldsc_jackknife.py} +0 -0
  82. /gwaslab/{ldsc_ldscore.py → extension/ldsc/ldsc_ldscore.py} +0 -0
  83. /gwaslab/{ldsc_parse.py → extension/ldsc/ldsc_parse.py} +0 -0
  84. /gwaslab/{prscs_gigrnd.py → extension/prscs/prscs_gigrnd.py} +0 -0
  85. /gwaslab/{prscs_parse_genet.py → extension/prscs/prscs_parse_genet.py} +0 -0
  86. /gwaslab/{hm_rsid_to_chrpos.py → hm/hm_rsid_to_chrpos.py} +0 -0
  87. /gwaslab/{io_process_args.py → io/io_process_args.py} +0 -0
  88. /gwaslab/{io_read_ldsc.py → io/io_read_ldsc.py} +0 -0
  89. /gwaslab/{qc_build.py → qc/qc_build.py} +0 -0
  90. /gwaslab/{qc_check_datatype.py → qc/qc_check_datatype.py} +0 -0
  91. /gwaslab/{util_ex_gwascatalog.py → util/util_ex_gwascatalog.py} +0 -0
  92. /gwaslab/{util_ex_infer_ancestry.py → util/util_ex_infer_ancestry.py} +0 -0
  93. /gwaslab/{util_ex_plink_filter.py → util/util_ex_plink_filter.py} +0 -0
  94. /gwaslab/{util_in_calculate_gc.py → util/util_in_calculate_gc.py} +0 -0
  95. /gwaslab/{util_in_calculate_power.py → util/util_in_calculate_power.py} +0 -0
  96. /gwaslab/{util_in_convert_h2.py → util/util_in_convert_h2.py} +0 -0
  97. /gwaslab/{util_in_correct_winnerscurse.py → util/util_in_correct_winnerscurse.py} +0 -0
  98. /gwaslab/{util_in_estimate_ess.py → util/util_in_estimate_ess.py} +0 -0
  99. /gwaslab/{util_in_get_density.py → util/util_in_get_density.py} +0 -0
  100. /gwaslab/{util_in_merge.py → util/util_in_merge.py} +0 -0
  101. /gwaslab/{util_in_snphwe.py → util/util_in_snphwe.py} +0 -0
  102. /gwaslab/{viz_aux_chromatin.py → viz/viz_aux_chromatin.py} +0 -0
  103. /gwaslab/{viz_aux_property.py → viz/viz_aux_property.py} +0 -0
  104. /gwaslab/{viz_aux_reposition_text.py → viz/viz_aux_reposition_text.py} +0 -0
  105. /gwaslab/{viz_aux_save_figure.py → viz/viz_aux_save_figure.py} +0 -0
  106. /gwaslab/{viz_plot_forestplot.py → viz/viz_plot_forestplot.py} +0 -0
  107. {gwaslab-3.6.5.dist-info → gwaslab-3.6.7.dist-info}/WHEEL +0 -0
  108. {gwaslab-3.6.5.dist-info → gwaslab-3.6.7.dist-info}/licenses/LICENSE +0 -0
  109. {gwaslab-3.6.5.dist-info → gwaslab-3.6.7.dist-info}/licenses/LICENSE_before_v3.4.39 +0 -0
  110. {gwaslab-3.6.5.dist-info → gwaslab-3.6.7.dist-info}/top_level.txt +0 -0
gwaslab/data/formatbook.json CHANGED
@@ -143,6 +143,7 @@
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  "format_separator": "\t",
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  "format_na": "#NA",
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  "format_comment": null,
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+ "format_assumption": "Note: auto-detection assumes A1=EA; Alt=EA and Frq=EAF",
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  "format_version": 20230328
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  },
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  "format_dict": {
@@ -330,7 +331,7 @@
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  "hm_beta": "BETA",
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  "hm_effect_allele_frequency": "EAF",
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  "standard_error": "SE",
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- "p-value": "P",
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+ "p_value": "P",
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  "hm_odds_ratio": "OR",
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  "hm_ci_lower": "OR_95L",
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  "hm_ci_upper": "OR_95U"
@@ -572,6 +573,324 @@
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  "z": "Z"
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  }
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  },
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+ "auto_1": {
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+ "meta_data": {
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+ "format_name": "auto_1",
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+ "format_separator": "\t",
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+ "format_na": "#NA",
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+ "format_comment": null,
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+ "format_assumption": "Note: auto-detection assumes A1=EA; ALT=EA and Frq=EAF",
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+ "format_version": 20250827
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+ },
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+ "format_dict": {
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+ "variant_id": "SNPID",
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+ "SNP": "SNPID",
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+ "snp": "SNPID",
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+ "SNPID": "SNPID",
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+ "snpid": "SNPID",
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+ "MARKERNAME": "SNPID",
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+ "MARKER": "SNPID",
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+ "markername": "SNPID",
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+ "marker": "SNPID",
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+ "RSID": "rsID",
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+ "rsid": "rsID",
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+ "hm_rsID": "rsID",
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+ "rsID": "SNPID",
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+ "chromosome": "CHR",
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+ "Chromosome": "CHR",
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+ "CHROMOSOME": "CHR",
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+ "CHR": "CHR",
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+ "chr": "CHR",
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+ "Chr": "CHR",
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+ "CHROM": "CHR",
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+ "Chrom": "CHR",
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+ "chrom": "CHR",
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+ "base_pair_location": "POS",
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+ "POS": "POS",
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+ "Pos": "POS",
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+ "pos": "POS",
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+ "BP": "POS",
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+ "bp": "POS",
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+ "bpos": "POS",
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+ "REF": "NEA",
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+ "Ref": "NEA",
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+ "reference_allele": "NEA",
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+ "reference": "NEA",
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+ "NEA": "NEA",
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+ "nea": "NEA",
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+ "non_effect_allele": "NEA",
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+ "NON_EFFECT_ALLELE": "NEA",
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+ "A0": "NEA",
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+ "a0": "NEA",
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+ "ALLELE0": "NEA",
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+ "Allele0": "NEA",
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+ "allele0": "NEA",
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+ "ALLELE_0": "NEA",
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+ "Allele_0": "NEA",
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+ "allele_0": "NEA",
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+ "A0FREQ": "NEAF",
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+ "A1": "EA",
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+ "a1": "EA",
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+ "ALLELE1": "EA",
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+ "Allele1": "EA",
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+ "allele1": "EA",
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+ "ALLELE_1": "EA",
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+ "Allele_1": "EA",
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+ "allele_1": "EA",
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+ "AF1": "EAF",
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+ "A2": "NEA",
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+ "a2": "NEA",
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+ "ALLELE2": "NEA",
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+ "Allele2": "NEA",
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+ "allele2": "NEA",
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+ "ALLELE_2": "NEA",
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+ "Allele_2": "NEA",
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+ "allele_2": "NEA",
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+ "AF2": "NEAF",
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+ "alternative_allele": "EA",
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+ "alternative": "EA",
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+ "Alt": "EA",
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+ "ALT": "EA",
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+ "effect_allele": "EA",
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+ "EA": "EA",
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+ "ea": "EA",
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+ "Frq": "EAF",
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+ "FRQ": "EAF",
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+ "frq": "EAF",
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+ "Frequency": "EAF",
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+ "FREQ": "EAF",
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+ "Freq": "EAF",
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+ "Freq0": "EAF",
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+ "freq": "EAF",
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+ "effect_allele_frequency": "EAF",
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+ "allelefrequency_effect": "EAF",
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+ "eaf": "EAF",
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+ "EAF": "EAF",
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+ "maf": "MAF",
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+ "Maf": "MAF",
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+ "MAF": "MAF",
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+ "n": "N",
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+ "N": "N",
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+ "sample_size": "N",
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+ "TotalSampleSize": "N",
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+ "Nsample": "N",
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+ "num_samples": "N",
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+ "Neff": "N_EFF",
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+ "N_EFF": "N_EFF",
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+ "N_CASE": "N_CASE",
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+ "Ncase": "N_CASE",
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+ "ncase": "N_CASE",
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+ "n_case": "N_CASE",
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+ "Ncontrol": "N_CONTROL",
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+ "N_control": "N_CONTROL",
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+ "N_Control": "N_CONTROL",
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+ "NCONTROL": "N_CONTROL",
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+ "beta": "BETA",
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+ "BETA": "BETA",
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+ "Beta": "BETA",
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+ "Effect": "BETA",
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+ "B": "BETA",
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+ "b": "BETA",
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+ "effect_weight": "BETA",
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+ "betase": "SE",
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+ "sebeta": "SE",
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+ "se": "SE",
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+ "SE": "SE",
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+ "standard_error": "SE",
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+ "StdErr": "SE",
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+ "p_value": "P",
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+ "PVAL": "P",
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+ "Pval": "P",
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+ "p": "P",
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+ "P": "P",
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+ "P.value": "P",
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+ "p.value": "P",
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+ "P_BOLT_LMM": "P",
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+ "neg_log_10_p_value": "MLOG10P",
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+ "MLOG10P": "MLOG10P",
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+ "LOG10_P": "MLOG10P",
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+ "chisq": "CHISQ",
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+ "chisq_association": "CHISQ",
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+ "CHISQ_BOLT_LMM": "CHISQ",
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+ "Z": "Z",
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+ "z": "Z",
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+ "Direction": "DIRECTION",
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+ "DIRECTION": "DIRECTION",
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+ "info": "INFO",
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+ "INFO": "INFO",
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+ "Rsq": "INFO",
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+ "R2": "INFO",
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+ "r2": "INFO",
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+ "imputationInfo": "INFO",
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+ "odds_ratio": "OR",
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+ "OR": "OR",
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+ "hazard_ratio": "HR",
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+ "ci_lower": "OR_95L",
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+ "OR_95L": "OR_95L",
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+ "ci_upper": "OR_95U",
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+ "OR_95U": "OR_95U",
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+ "STATUS": "STATUS"
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+ }
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+ },
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+ "auto_2": {
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+ "meta_data": {
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+ "format_name": "auto_2",
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+ "format_separator": "\t",
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+ "format_na": "#NA",
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+ "format_comment": null,
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+ "format_assumption": "Note: auto-detection assumes A2=EA; ALT=EA and Frq=EAF",
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+ "format_version": 20250827
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+ },
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+ "format_dict": {
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+ "variant_id": "SNPID",
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+ "SNP": "SNPID",
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+ "snp": "SNPID",
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+ "SNPID": "SNPID",
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+ "snpid": "SNPID",
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+ "MARKERNAME": "SNPID",
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+ "MARKER": "SNPID",
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+ "markername": "SNPID",
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+ "marker": "SNPID",
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+ "RSID": "rsID",
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+ "rsid": "rsID",
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+ "hm_rsID": "rsID",
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+ "rsID": "SNPID",
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+ "chromosome": "CHR",
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+ "Chromosome": "CHR",
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+ "CHROMOSOME": "CHR",
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+ "CHR": "CHR",
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+ "chr": "CHR",
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+ "Chr": "CHR",
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+ "CHROM": "CHR",
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+ "Chrom": "CHR",
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+ "chrom": "CHR",
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+ "base_pair_location": "POS",
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+ "POS": "POS",
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+ "Pos": "POS",
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+ "pos": "POS",
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+ "BP": "POS",
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+ "bp": "POS",
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+ "bpos": "POS",
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+ "REF": "NEA",
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+ "Ref": "NEA",
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+ "reference_allele": "NEA",
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+ "reference": "NEA",
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+ "NEA": "NEA",
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+ "nea": "NEA",
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+ "non_effect_allele": "NEA",
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+ "NON_EFFECT_ALLELE": "NEA",
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+ "A0": "NEA",
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+ "a0": "NEA",
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+ "ALLELE0": "NEA",
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+ "Allele0": "NEA",
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+ "allele0": "NEA",
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+ "ALLELE_0": "NEA",
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+ "Allele_0": "NEA",
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+ "allele_0": "NEA",
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+ "A0FREQ": "NEAF",
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+ "A1": "NEA",
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+ "a1": "NEA",
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+ "ALLELE1": "NEA",
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+ "Allele1": "NEA",
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+ "allele1": "NEA",
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+ "ALLELE_1": "NEA",
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+ "Allele_1": "NEA",
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+ "allele_1": "NEA",
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+ "AF1": "NEAF",
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+ "A2": "EA",
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+ "a2": "EA",
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+ "ALLELE2": "EA",
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+ "Allele2": "EA",
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+ "allele2": "EA",
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+ "ALLELE_2": "EA",
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+ "Allele_2": "EA",
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+ "allele_2": "EA",
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+ "AF2": "EAF",
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+ "alternative_allele": "EA",
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+ "alternative": "EA",
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+ "Alt": "EA",
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+ "ALT": "EA",
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+ "effect_allele": "EA",
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+ "EA": "EA",
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+ "ea": "EA",
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+ "Frq": "EAF",
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+ "FRQ": "EAF",
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+ "frq": "EAF",
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+ "Frequency": "EAF",
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+ "FREQ": "EAF",
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+ "Freq": "EAF",
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+ "Freq0": "EAF",
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+ "freq": "EAF",
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+ "effect_allele_frequency": "EAF",
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+ "allelefrequency_effect": "EAF",
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+ "eaf": "EAF",
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+ "EAF": "EAF",
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+ "maf": "MAF",
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+ "Maf": "MAF",
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+ "MAF": "MAF",
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+ "n": "N",
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+ "N": "N",
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+ "sample_size": "N",
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+ "TotalSampleSize": "N",
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+ "Nsample": "N",
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+ "num_samples": "N",
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+ "Neff": "N_EFF",
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+ "N_EFF": "N_EFF",
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+ "N_CASE": "N_CASE",
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+ "Ncase": "N_CASE",
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+ "ncase": "N_CASE",
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+ "n_case": "N_CASE",
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+ "Ncontrol": "N_CONTROL",
844
+ "N_control": "N_CONTROL",
845
+ "N_Control": "N_CONTROL",
846
+ "NCONTROL": "N_CONTROL",
847
+ "beta": "BETA",
848
+ "BETA": "BETA",
849
+ "Beta": "BETA",
850
+ "Effect": "BETA",
851
+ "B": "BETA",
852
+ "b": "BETA",
853
+ "effect_weight": "BETA",
854
+ "betase": "SE",
855
+ "sebeta": "SE",
856
+ "se": "SE",
857
+ "SE": "SE",
858
+ "standard_error": "SE",
859
+ "StdErr": "SE",
860
+ "p_value": "P",
861
+ "PVAL": "P",
862
+ "Pval": "P",
863
+ "p": "P",
864
+ "P": "P",
865
+ "P.value": "P",
866
+ "p.value": "P",
867
+ "P_BOLT_LMM": "P",
868
+ "neg_log_10_p_value": "MLOG10P",
869
+ "MLOG10P": "MLOG10P",
870
+ "LOG10_P": "MLOG10P",
871
+ "chisq": "CHISQ",
872
+ "chisq_association": "CHISQ",
873
+ "CHISQ_BOLT_LMM": "CHISQ",
874
+ "Z": "Z",
875
+ "z": "Z",
876
+ "Direction": "DIRECTION",
877
+ "DIRECTION": "DIRECTION",
878
+ "info": "INFO",
879
+ "INFO": "INFO",
880
+ "Rsq": "INFO",
881
+ "R2": "INFO",
882
+ "r2": "INFO",
883
+ "imputationInfo": "INFO",
884
+ "odds_ratio": "OR",
885
+ "OR": "OR",
886
+ "hazard_ratio": "HR",
887
+ "ci_lower": "OR_95L",
888
+ "OR_95L": "OR_95L",
889
+ "ci_upper": "OR_95U",
890
+ "OR_95U": "OR_95U",
891
+ "STATUS": "STATUS"
892
+ }
893
+ },
575
894
  "pgscatalog_hm": {
576
895
  "meta_data": {
577
896
  "format_name": "pgscatalog_hm Harmonized File",
@@ -590,6 +909,164 @@
590
909
  "OR": "OR"
591
910
  }
592
911
  },
912
+ "auto_neaf": {
913
+ "meta_data": {
914
+ "format_name": "auto_neaf",
915
+ "format_separator": "\t",
916
+ "format_na": "#NA",
917
+ "format_comment": null,
918
+ "format_assumption": "Note: auto-detection assumes A1=EA; ALT=EA and Frq=NEAF",
919
+ "format_version": 20250827
920
+ },
921
+ "format_dict": {
922
+ "variant_id": "SNPID",
923
+ "SNP": "SNPID",
924
+ "snp": "SNPID",
925
+ "SNPID": "SNPID",
926
+ "snpid": "SNPID",
927
+ "MARKERNAME": "SNPID",
928
+ "MARKER": "SNPID",
929
+ "markername": "SNPID",
930
+ "marker": "SNPID",
931
+ "RSID": "rsID",
932
+ "rsid": "rsID",
933
+ "hm_rsID": "rsID",
934
+ "rsID": "SNPID",
935
+ "chromosome": "CHR",
936
+ "Chromosome": "CHR",
937
+ "CHROMOSOME": "CHR",
938
+ "CHR": "CHR",
939
+ "chr": "CHR",
940
+ "Chr": "CHR",
941
+ "CHROM": "CHR",
942
+ "Chrom": "CHR",
943
+ "chrom": "CHR",
944
+ "base_pair_location": "POS",
945
+ "POS": "POS",
946
+ "Pos": "POS",
947
+ "pos": "POS",
948
+ "BP": "POS",
949
+ "bp": "POS",
950
+ "bpos": "POS",
951
+ "REF": "NEA",
952
+ "Ref": "NEA",
953
+ "reference_allele": "NEA",
954
+ "reference": "NEA",
955
+ "NEA": "NEA",
956
+ "nea": "NEA",
957
+ "non_effect_allele": "NEA",
958
+ "NON_EFFECT_ALLELE": "NEA",
959
+ "A0": "NEA",
960
+ "a0": "NEA",
961
+ "ALLELE0": "NEA",
962
+ "Allele0": "NEA",
963
+ "allele0": "NEA",
964
+ "ALLELE_0": "NEA",
965
+ "Allele_0": "NEA",
966
+ "allele_0": "NEA",
967
+ "A2": "NEA",
968
+ "a2": "NEA",
969
+ "ALLELE2": "NEA",
970
+ "Allele2": "NEA",
971
+ "allele2": "NEA",
972
+ "ALLELE_2": "NEA",
973
+ "Allele_2": "NEA",
974
+ "allele_2": "NEA",
975
+ "alternative_allele": "EA",
976
+ "alternative": "EA",
977
+ "Alt": "EA",
978
+ "ALT": "EA",
979
+ "A1": "EA",
980
+ "a1": "EA",
981
+ "effect_allele": "EA",
982
+ "EA": "EA",
983
+ "ea": "EA",
984
+ "ALLELE1": "EA",
985
+ "Allele1": "EA",
986
+ "allele1": "EA",
987
+ "ALLELE_1": "EA",
988
+ "Allele_1": "EA",
989
+ "allele_1": "EA",
990
+ "Frq": "NEAF",
991
+ "FRQ": "NEAF",
992
+ "frq": "NEAF",
993
+ "Frequency": "NEAF",
994
+ "FREQ": "NEAF",
995
+ "Freq": "NEAF",
996
+ "freq": "NEAF",
997
+ "Freq1": "EAF",
998
+ "A1FREQ": "EAF",
999
+ "effect_allele_frequency": "EAF",
1000
+ "allelefrequency_effect": "EAF",
1001
+ "eaf": "EAF",
1002
+ "EAF": "EAF",
1003
+ "AF1": "EAF",
1004
+ "maf": "MAF",
1005
+ "Maf": "MAF",
1006
+ "MAF": "MAF",
1007
+ "n": "N",
1008
+ "N": "N",
1009
+ "sample_size": "N",
1010
+ "TotalSampleSize": "N",
1011
+ "Nsample": "N",
1012
+ "num_samples": "N",
1013
+ "Neff": "N_EFF",
1014
+ "N_EFF": "N_EFF",
1015
+ "N_CASE": "N_CASE",
1016
+ "Ncase": "N_CASE",
1017
+ "ncase": "N_CASE",
1018
+ "n_case": "N_CASE",
1019
+ "Ncontrol": "N_CONTROL",
1020
+ "N_control": "N_CONTROL",
1021
+ "N_Control": "N_CONTROL",
1022
+ "NCONTROL": "N_CONTROL",
1023
+ "beta": "BETA",
1024
+ "BETA": "BETA",
1025
+ "Beta": "BETA",
1026
+ "Effect": "BETA",
1027
+ "B": "BETA",
1028
+ "b": "BETA",
1029
+ "effect_weight": "BETA",
1030
+ "betase": "SE",
1031
+ "sebeta": "SE",
1032
+ "se": "SE",
1033
+ "SE": "SE",
1034
+ "standard_error": "SE",
1035
+ "StdErr": "SE",
1036
+ "p_value": "P",
1037
+ "PVAL": "P",
1038
+ "Pval": "P",
1039
+ "p": "P",
1040
+ "P": "P",
1041
+ "P.value": "P",
1042
+ "p.value": "P",
1043
+ "P_BOLT_LMM": "P",
1044
+ "neg_log_10_p_value": "MLOG10P",
1045
+ "MLOG10P": "MLOG10P",
1046
+ "LOG10_P": "MLOG10P",
1047
+ "chisq": "CHISQ",
1048
+ "chisq_association": "CHISQ",
1049
+ "CHISQ_BOLT_LMM": "CHISQ",
1050
+ "Z": "Z",
1051
+ "z": "Z",
1052
+ "Direction": "DIRECTION",
1053
+ "DIRECTION": "DIRECTION",
1054
+ "info": "INFO",
1055
+ "INFO": "INFO",
1056
+ "Rsq": "INFO",
1057
+ "R2": "INFO",
1058
+ "r2": "INFO",
1059
+ "imputationInfo": "INFO",
1060
+ "odds_ratio": "OR",
1061
+ "OR": "OR",
1062
+ "hazard_ratio": "HR",
1063
+ "ci_lower": "OR_95L",
1064
+ "OR_95L": "OR_95L",
1065
+ "ci_upper": "OR_95U",
1066
+ "OR_95U": "OR_95U",
1067
+ "STATUS": "STATUS"
1068
+ }
1069
+ },
593
1070
  "regenie": {
594
1071
  "meta_data": {
595
1072
  "format_name": "regenie",
@@ -680,17 +1157,177 @@
680
1157
  "REF": "REF",
681
1158
  "ALT": "ALT",
682
1159
  "A1": "EA",
683
- "OBS_CT": "N",
684
- "A1_FREQ": "EAF",
1160
+ "OBS_CT": "N",
1161
+ "A1_FREQ": "EAF",
1162
+ "BETA": "BETA",
1163
+ "LOG(OR)_SE": "SE",
1164
+ "SE": "SE",
1165
+ "T_STAT": "T",
1166
+ "Z_STAT": "Z",
1167
+ "P": "P",
1168
+ "LOG10_P": "MLOG10P",
1169
+ "MACH_R2": "INFO",
1170
+ "OR": "OR"
1171
+ }
1172
+ },
1173
+ "auto_ref": {
1174
+ "meta_data": {
1175
+ "format_name": "auto",
1176
+ "format_separator": "\t",
1177
+ "format_na": "#NA",
1178
+ "format_comment": null,
1179
+ "format_assumption": "Note: auto-detection assumes A1=EA; REF=EA and Frq=EAF",
1180
+ "format_version": 20230328
1181
+ },
1182
+ "format_dict": {
1183
+ "variant_id": "SNPID",
1184
+ "SNP": "SNPID",
1185
+ "snp": "SNPID",
1186
+ "SNPID": "SNPID",
1187
+ "snpid": "SNPID",
1188
+ "MARKERNAME": "SNPID",
1189
+ "MARKER": "SNPID",
1190
+ "markername": "SNPID",
1191
+ "marker": "SNPID",
1192
+ "RSID": "rsID",
1193
+ "rsid": "rsID",
1194
+ "hm_rsID": "rsID",
1195
+ "rsID": "SNPID",
1196
+ "chromosome": "CHR",
1197
+ "Chromosome": "CHR",
1198
+ "CHROMOSOME": "CHR",
1199
+ "CHR": "CHR",
1200
+ "chr": "CHR",
1201
+ "Chr": "CHR",
1202
+ "CHROM": "CHR",
1203
+ "Chrom": "CHR",
1204
+ "chrom": "CHR",
1205
+ "base_pair_location": "POS",
1206
+ "POS": "POS",
1207
+ "Pos": "POS",
1208
+ "pos": "POS",
1209
+ "BP": "POS",
1210
+ "bp": "POS",
1211
+ "bpos": "POS",
1212
+ "REF": "EA",
1213
+ "Ref": "EA",
1214
+ "reference_allele": "EA",
1215
+ "reference": "EA",
1216
+ "reference_allele_frequency": "EAF",
1217
+ "NEA": "NEA",
1218
+ "nea": "NEA",
1219
+ "non_effect_allele": "NEA",
1220
+ "NON_EFFECT_ALLELE": "NEA",
1221
+ "A0": "NEA",
1222
+ "a0": "NEA",
1223
+ "ALLELE0": "NEA",
1224
+ "Allele0": "NEA",
1225
+ "allele0": "NEA",
1226
+ "ALLELE_0": "NEA",
1227
+ "Allele_0": "NEA",
1228
+ "allele_0": "NEA",
1229
+ "A2": "NEA",
1230
+ "a2": "NEA",
1231
+ "ALLELE2": "NEA",
1232
+ "Allele2": "NEA",
1233
+ "allele2": "NEA",
1234
+ "ALLELE_2": "NEA",
1235
+ "Allele_2": "NEA",
1236
+ "allele_2": "NEA",
1237
+ "alternative_allele": "NEA",
1238
+ "alternative": "NEA",
1239
+ "Alt": "NEA",
1240
+ "ALT": "NEA",
1241
+ "alternative_allele_frequency": "NEAF",
1242
+ "A1": "EA",
1243
+ "a1": "EA",
1244
+ "effect_allele": "EA",
1245
+ "EA": "EA",
1246
+ "ea": "EA",
1247
+ "ALLELE1": "EA",
1248
+ "Allele1": "EA",
1249
+ "allele1": "EA",
1250
+ "ALLELE_1": "EA",
1251
+ "Allele_1": "EA",
1252
+ "allele_1": "EA",
1253
+ "Frq": "EAF",
1254
+ "FRQ": "EAF",
1255
+ "frq": "EAF",
1256
+ "Frequency": "EAF",
1257
+ "FREQ": "EAF",
1258
+ "Freq": "EAF",
1259
+ "Freq1": "EAF",
1260
+ "freq": "EAF",
1261
+ "A1FREQ": "EAF",
1262
+ "effect_allele_frequency": "EAF",
1263
+ "allelefrequency_effect": "EAF",
1264
+ "eaf": "EAF",
1265
+ "EAF": "EAF",
1266
+ "AF1": "EAF",
1267
+ "maf": "MAF",
1268
+ "Maf": "MAF",
1269
+ "MAF": "MAF",
1270
+ "n": "N",
1271
+ "N": "N",
1272
+ "sample_size": "N",
1273
+ "TotalSampleSize": "N",
1274
+ "Nsample": "N",
1275
+ "num_samples": "N",
1276
+ "Neff": "N_EFF",
1277
+ "N_EFF": "N_EFF",
1278
+ "N_CASE": "N_CASE",
1279
+ "Ncase": "N_CASE",
1280
+ "ncase": "N_CASE",
1281
+ "n_case": "N_CASE",
1282
+ "Ncontrol": "N_CONTROL",
1283
+ "N_control": "N_CONTROL",
1284
+ "N_Control": "N_CONTROL",
1285
+ "NCONTROL": "N_CONTROL",
1286
+ "beta": "BETA",
685
1287
  "BETA": "BETA",
686
- "LOG(OR)_SE": "SE",
1288
+ "Beta": "BETA",
1289
+ "Effect": "BETA",
1290
+ "B": "BETA",
1291
+ "b": "BETA",
1292
+ "effect_weight": "BETA",
1293
+ "betase": "SE",
1294
+ "sebeta": "SE",
1295
+ "se": "SE",
687
1296
  "SE": "SE",
688
- "T_STAT": "T",
689
- "Z_STAT": "Z",
1297
+ "standard_error": "SE",
1298
+ "StdErr": "SE",
1299
+ "p_value": "P",
1300
+ "PVAL": "P",
1301
+ "Pval": "P",
1302
+ "p": "P",
690
1303
  "P": "P",
1304
+ "P.value": "P",
1305
+ "p.value": "P",
1306
+ "P_BOLT_LMM": "P",
1307
+ "neg_log_10_p_value": "MLOG10P",
1308
+ "MLOG10P": "MLOG10P",
691
1309
  "LOG10_P": "MLOG10P",
692
- "MACH_R2": "INFO",
693
- "OR": "OR"
1310
+ "chisq": "CHISQ",
1311
+ "chisq_association": "CHISQ",
1312
+ "CHISQ_BOLT_LMM": "CHISQ",
1313
+ "Z": "Z",
1314
+ "z": "Z",
1315
+ "Direction": "DIRECTION",
1316
+ "DIRECTION": "DIRECTION",
1317
+ "info": "INFO",
1318
+ "INFO": "INFO",
1319
+ "Rsq": "INFO",
1320
+ "R2": "INFO",
1321
+ "r2": "INFO",
1322
+ "imputationInfo": "INFO",
1323
+ "odds_ratio": "OR",
1324
+ "OR": "OR",
1325
+ "hazard_ratio": "HR",
1326
+ "ci_lower": "OR_95L",
1327
+ "OR_95L": "OR_95L",
1328
+ "ci_upper": "OR_95U",
1329
+ "OR_95U": "OR_95U",
1330
+ "STATUS": "STATUS"
694
1331
  }
695
1332
  },
696
1333
  "gwaslab": {
@@ -883,6 +1520,165 @@
883
1520
  "U95": "OR_95U"
884
1521
  }
885
1522
  },
1523
+ "auto_0": {
1524
+ "meta_data": {
1525
+ "format_name": "auto_0",
1526
+ "format_separator": "\t",
1527
+ "format_na": "#NA",
1528
+ "format_comment": null,
1529
+ "format_assumption": "Note: auto-detection assumes A0=EA; ALT=EA and Frq=EAF",
1530
+ "format_version": 20250827
1531
+ },
1532
+ "format_dict": {
1533
+ "variant_id": "SNPID",
1534
+ "SNP": "SNPID",
1535
+ "snp": "SNPID",
1536
+ "SNPID": "SNPID",
1537
+ "snpid": "SNPID",
1538
+ "MARKERNAME": "SNPID",
1539
+ "MARKER": "SNPID",
1540
+ "markername": "SNPID",
1541
+ "marker": "SNPID",
1542
+ "RSID": "rsID",
1543
+ "rsid": "rsID",
1544
+ "hm_rsID": "rsID",
1545
+ "rsID": "SNPID",
1546
+ "chromosome": "CHR",
1547
+ "Chromosome": "CHR",
1548
+ "CHROMOSOME": "CHR",
1549
+ "CHR": "CHR",
1550
+ "chr": "CHR",
1551
+ "Chr": "CHR",
1552
+ "CHROM": "CHR",
1553
+ "Chrom": "CHR",
1554
+ "chrom": "CHR",
1555
+ "base_pair_location": "POS",
1556
+ "POS": "POS",
1557
+ "Pos": "POS",
1558
+ "pos": "POS",
1559
+ "BP": "POS",
1560
+ "bp": "POS",
1561
+ "bpos": "POS",
1562
+ "REF": "NEA",
1563
+ "Ref": "NEA",
1564
+ "reference_allele": "NEA",
1565
+ "reference": "NEA",
1566
+ "NEA": "NEA",
1567
+ "nea": "NEA",
1568
+ "non_effect_allele": "NEA",
1569
+ "NON_EFFECT_ALLELE": "NEA",
1570
+ "A0": "EA",
1571
+ "a0": "EA",
1572
+ "ALLELE0": "EA",
1573
+ "Allele0": "EA",
1574
+ "allele0": "EA",
1575
+ "ALLELE_0": "EA",
1576
+ "Allele_0": "EA",
1577
+ "allele_0": "EA",
1578
+ "A0FREQ": "EAF",
1579
+ "A1": "NEA",
1580
+ "a1": "NEA",
1581
+ "ALLELE1": "NEA",
1582
+ "Allele1": "NEA",
1583
+ "allele1": "NEA",
1584
+ "ALLELE_1": "NEA",
1585
+ "Allele_1": "NEA",
1586
+ "allele_1": "NEA",
1587
+ "AF1": "NEAF",
1588
+ "A2": "NEA",
1589
+ "a2": "NEA",
1590
+ "ALLELE2": "NEA",
1591
+ "Allele2": "NEA",
1592
+ "allele2": "NEA",
1593
+ "ALLELE_2": "NEA",
1594
+ "Allele_2": "NEA",
1595
+ "allele_2": "NEA",
1596
+ "AF2": "NEAF",
1597
+ "alternative_allele": "EA",
1598
+ "alternative": "EA",
1599
+ "Alt": "EA",
1600
+ "ALT": "EA",
1601
+ "effect_allele": "EA",
1602
+ "EA": "EA",
1603
+ "ea": "EA",
1604
+ "Frq": "EAF",
1605
+ "FRQ": "EAF",
1606
+ "frq": "EAF",
1607
+ "Frequency": "EAF",
1608
+ "FREQ": "EAF",
1609
+ "Freq": "EAF",
1610
+ "Freq0": "EAF",
1611
+ "freq": "EAF",
1612
+ "effect_allele_frequency": "EAF",
1613
+ "allelefrequency_effect": "EAF",
1614
+ "eaf": "EAF",
1615
+ "EAF": "EAF",
1616
+ "maf": "MAF",
1617
+ "Maf": "MAF",
1618
+ "MAF": "MAF",
1619
+ "n": "N",
1620
+ "N": "N",
1621
+ "sample_size": "N",
1622
+ "TotalSampleSize": "N",
1623
+ "Nsample": "N",
1624
+ "num_samples": "N",
1625
+ "Neff": "N_EFF",
1626
+ "N_EFF": "N_EFF",
1627
+ "N_CASE": "N_CASE",
1628
+ "Ncase": "N_CASE",
1629
+ "ncase": "N_CASE",
1630
+ "n_case": "N_CASE",
1631
+ "Ncontrol": "N_CONTROL",
1632
+ "N_control": "N_CONTROL",
1633
+ "N_Control": "N_CONTROL",
1634
+ "NCONTROL": "N_CONTROL",
1635
+ "beta": "BETA",
1636
+ "BETA": "BETA",
1637
+ "Beta": "BETA",
1638
+ "Effect": "BETA",
1639
+ "B": "BETA",
1640
+ "b": "BETA",
1641
+ "effect_weight": "BETA",
1642
+ "betase": "SE",
1643
+ "sebeta": "SE",
1644
+ "se": "SE",
1645
+ "SE": "SE",
1646
+ "standard_error": "SE",
1647
+ "StdErr": "SE",
1648
+ "p_value": "P",
1649
+ "PVAL": "P",
1650
+ "Pval": "P",
1651
+ "p": "P",
1652
+ "P": "P",
1653
+ "P.value": "P",
1654
+ "p.value": "P",
1655
+ "P_BOLT_LMM": "P",
1656
+ "neg_log_10_p_value": "MLOG10P",
1657
+ "MLOG10P": "MLOG10P",
1658
+ "LOG10_P": "MLOG10P",
1659
+ "chisq": "CHISQ",
1660
+ "chisq_association": "CHISQ",
1661
+ "CHISQ_BOLT_LMM": "CHISQ",
1662
+ "Z": "Z",
1663
+ "z": "Z",
1664
+ "Direction": "DIRECTION",
1665
+ "DIRECTION": "DIRECTION",
1666
+ "info": "INFO",
1667
+ "INFO": "INFO",
1668
+ "Rsq": "INFO",
1669
+ "R2": "INFO",
1670
+ "r2": "INFO",
1671
+ "imputationInfo": "INFO",
1672
+ "odds_ratio": "OR",
1673
+ "OR": "OR",
1674
+ "hazard_ratio": "HR",
1675
+ "ci_lower": "OR_95L",
1676
+ "OR_95L": "OR_95L",
1677
+ "ci_upper": "OR_95U",
1678
+ "OR_95U": "OR_95U",
1679
+ "STATUS": "STATUS"
1680
+ }
1681
+ },
886
1682
  "template": {
887
1683
  "meta_data": {
888
1684
  "format_name": "",
@@ -1026,7 +1822,7 @@
1026
1822
  "beta": "BETA",
1027
1823
  "effect_allele_frequency": "EAF",
1028
1824
  "standard_error": "SE",
1029
- "p-value": "P",
1825
+ "p_value": "P",
1030
1826
  "odds_ratio": "OR",
1031
1827
  "ci_lower": "OR_95L",
1032
1828
  "ci_upper": "OR_95U"