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4957 lines (4957 loc) · 164 KB
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{
"tensorqtl_cis_nominal_interaction": {
"meta_data": {
"format_name": "tensorqtl_cis_nominal_interaction",
"format_source": "https://raw.githubusercontent.com/broadinstitute/tensorqtl/refs/heads/master/docs/outputs.md",
"format_version": "20220726",
"format_cite_name": "tensorQTL",
"format_description": "tensorQTL cis-nominal mode with interaction term output format"
},
"format_dict": {
"variant_id": "SNPID",
"phenotype_id": "TRAIT",
"start_distance": "START_DISTANCE",
"end_distance": "END_DISTANCE",
"af": "EAF",
"ma_samples": "MA_SAMPLES",
"ma_count": "MA_COUNT",
"pval_g": "P_G",
"b_g": "BETA_G",
"b_g_se": "SE_G",
"pval_i": "P_I",
"b_i": "BETA_I",
"b_i_se": "SE_I",
"pval_gi": "P_GI",
"b_gi": "BETA_GI",
"b_gi_se": "SE_GI",
"tests_emt": "TESTS_EMT",
"pval_emt": "P_EMT",
"pval_adj_bh": "P_ADJ_BH"
},
"header_description": {
"phenotype_id": "Phenotype ID",
"variant_id": "Variant ID",
"start_distance": "Distance between the variant and phenotype start position (e.g., TSS)",
"end_distance": "Distance between the variant and phenotype end position (only present if different from start position)",
"af": "In-sample ALT allele frequency of the variant",
"ma_samples": "Number of samples carrying at least one minor allele",
"ma_count": "Number of minor alleles",
"pval_g": "Nominal p-value of the genotype term",
"b_g": "Slope of the genotype term",
"b_g_se": "Standard error of b_g",
"pval_i": "Nominal p-value of the interaction variable",
"b_i": "Slope of the interaction variable",
"b_i_se": "Standard error of b_i",
"pval_gi": "Nominal p-value of the interaction term",
"b_gi": "Slope of the interaction term",
"b_gi_se": "Standard error of b_gi",
"tests_emt": "Effective number of independent variants (M_eff) estimated by eigenMT",
"pval_emt": "Bonferroni-adjusted pval_gi (i.e., multiplied by M_eff)",
"pval_adj_bh": "Benjamini-Hochberg adjusted pval_emt"
}
},
"metal": {
"meta_data": {
"format_name": "metal",
"format_source": "https://genome.sph.umich.edu/wiki/METAL_Documentation",
"format_version": "20220726"
},
"format_dict": {
"MarkerName": "SNPID",
"Allele1": "EA",
"Allele2": "NEA",
"Freq1": "EAF",
"Effect": "BETA",
"StdErr": "SE",
"P-value": "P",
"Direction": "DIRECTION"
}
},
"gwascatalog_hm": {
"meta_data": {
"format_name": "gwascatalog_hm",
"format_source": "https://www.ebi.ac.uk/gwas/docs/methods/summary-statistics",
"format_version": 20220806
},
"format_dict": {
"hm_variant_id": "SNPID",
"chromosome": "CHR",
"base_pair_location": "POS",
"hm_other_allele": "NEA",
"hm_effect_allele": "EA",
"hm_beta": "BETA",
"hm_effect_allele_frequency": "EAF",
"standard_error": "SE",
"p_value": "P",
"hm_odds_ratio": "OR",
"hm_ci_lower": "OR_95L",
"hm_ci_upper": "OR_95U"
}
},
"gwascatalog": {
"meta_data": {
"format_name": "gwascatalog",
"format_source": "https://www.ebi.ac.uk/gwas/docs/methods/summary-statistics",
"format_version": "20220726"
},
"format_dict": {
"variant_id": "SNPID",
"chromosome": "CHR",
"base_pair_location": "POS",
"other_allele": "NEA",
"effect_allele": "EA",
"beta": "BETA",
"effect_allele_frequency": "EAF",
"standard_error": "SE",
"p_value": "P",
"odds_ratio": "OR",
"ci_lower": "OR_95L",
"ci_upper": "OR_95U"
}
},
"mesusie": {
"meta_data": {
"format_name": "MESuSiE",
"format_source": "https://borangao.github.io/meSuSie_Analysis/installation.html",
"format_version": 20221109
},
"format_dict": {
"SNP": "SNPID",
"N": "N",
"Beta": "BETA",
"Se": "SE",
"Z": "Z",
"POS": "POS"
}
},
"plink_pvar": {
"meta_data": {
"format_name": ".pvar",
"format_source": "https://www.cog-genomics.org/plink/2.0/formats#pvar",
"format_version": "PLINK 2.0 (doc revision 11 Mar 2026)",
"format_cite_name": "PLINK 2.0",
"format_description": "Variant table for .pgen; VCF-style headers allowed. Last header line starts with '#CHROM'. Without headers, columns follow .bim order (CHROM, ID, CM, POS, ALT, REF or 5-column without CM).",
"format_separator": "\t",
"format_na": ".",
"format_comment": "#",
"format_header": true,
"format_datatype": {
"#CHROM": "category",
"CHROM": "category",
"POS": "int",
"ID": "string",
"REF": "string",
"ALT": "string",
"QUAL": "float",
"FILTER": "string",
"INFO": "string"
},
"format_col_order": [
"#CHROM",
"POS",
"ID",
"REF",
"ALT",
"QUAL",
"FILTER",
"INFO",
"FORMAT",
"CM"
],
"last_check_date": "20260326"
},
"format_dict": {
"#CHROM": "CHR",
"CHROM": "CHR",
"POS": "POS",
"ID": "SNPID",
"REF": "REF",
"ALT": "ALT",
"QUAL": "QUAL",
"FILTER": "FILTER",
"INFO": "INFO",
"FORMAT": "FORMAT",
"CM": "CM"
},
"format_dict_2": {
"ID": "rsID"
},
"header_description": {
"#CHROM": "Chromosome code",
"POS": "Base-pair coordinate",
"ID": "Variant ID",
"REF": "Reference allele",
"ALT": "Alternate alleles (comma-separated)",
"QUAL": "Phred-scaled locus quality",
"FILTER": "FILTER field",
"INFO": "INFO field",
"FORMAT": "FORMAT column when present",
"CM": "Centimorgan position (optional)"
}
},
"bgenie": {
"meta_data": {
"format_name": "bgenie",
"format_source": "https://jmarchini.org/bgenie/",
"format_version": "latest",
"format_separator": " ",
"format_comment": "BGENIE output is space-separated and gzip compressed. Phenotype-specific columns follow the pattern {pheno_name}_beta, {pheno_name}_se, {pheno_name}_t, and optionally {pheno_name}_p (if --pvals flag is used). The beta coefficient refers to the effect of having an extra copy of a_1 (the second allele)."
},
"format_dict": {
"chr": "CHR",
"rsid": "rsID",
"pos": "POS",
"a_0": "NEA",
"a_1": "EA",
"af": "EAF",
"info": "INFO",
"pheno1_beta": "BETA",
"pheno1_se": "SE",
"pheno1_t": "T",
"pheno1_p": "MLOG10P"
}
},
"plink": {
"meta_data": {
"format_name": "plink1_assoc_outputs",
"format_source": "https://www.cog-genomics.org/plink/1.9/formats",
"format_version": "PLINK 1.9 (doc revision 19 Aug 2025)",
"format_citation": "Purcell, S., Neale, B., Todd-Brown, K., Thomas, L., Ferreira, M. A., Bender, D., ... & Sham, P. C. (2007). PLINK: a tool set for whole-genome association and population-based linkage analyses. The American journal of human genetics, 81(3), 559-575.",
"format_cite_name": "PLINK 1.9",
"format_description": "Union of common association columns across .assoc, .assoc.fisher, .assoc.linear, .assoc.logistic, and .assoc.dosage; see per-extension specs in formats/plink_*.json.",
"format_separator": "\t",
"format_na": null,
"format_comment": null,
"format_header": true,
"last_check_date": "20260326"
},
"format_dict": {
"SNP": "SNPID",
"CHR": "CHR",
"BP": "POS",
"A2": "NEA",
"A1": "EA",
"F_A": "EAF_CASE",
"F_U": "EAF_CONTROL",
"FRQ": "EAF",
"FRQ_A": "EAF_CASE",
"FRQ_U": "EAF_CONTROL",
"BETA": "BETA",
"OR": "OR",
"SE": "SE",
"P": "P",
"INFO": "INFO",
"STAT": "T",
"CHISQ": "CHISQ",
"NMISS": "N"
},
"format_dict_2": {
"SNP": "rsID"
}
},
"plink_logistic": {
"meta_data": {
"format_name": ".assoc.logistic",
"format_source": "https://www.cog-genomics.org/plink/1.9/formats#assoc_linear",
"format_version": "PLINK 1.9 (doc revision 19 Aug 2025)",
"format_citation": "Purcell, S., Neale, B., Todd-Brown, K., Thomas, L., Ferreira, M. A., Bender, D., ... & Sham, P. C. (2007). PLINK: a tool set for whole-genome association and population-based linkage analyses. The American journal of human genetics, 81(3), 559-575.",
"format_cite_name": "PLINK 1.9",
"format_description": "Multi-covariate logistic regression from --logistic. BETA column appears with '--logistic beta'; otherwise OR. With --ci 0.xy, SE, L_xy, U_xy are inserted before STAT (SE is on log-odds scale).",
"format_separator": "\t",
"format_na": null,
"format_comment": null,
"format_header": true,
"format_col_order": [
"CHR",
"SNP",
"BP",
"A1",
"TEST",
"NMISS",
"OR",
"BETA",
"SE",
"L95",
"U95",
"STAT",
"P"
],
"last_check_date": "20260326"
},
"format_dict": {
"CHR": "CHR",
"SNP": "SNPID",
"BP": "POS",
"A1": "EA",
"A2": "NEA",
"TEST": null,
"NMISS": "N",
"OR": "OR",
"BETA": "BETA",
"SE": "SE",
"L95": "OR_95L",
"U95": "OR_95U",
"STAT": "T",
"P": "P",
"CHISQ": "CHISQ"
},
"format_dict_2": {
"SNP": "rsID"
},
"header_description": {
"CHR": "Chromosome code (omitted with 'no-snp')",
"SNP": "Variant identifier (omitted with 'no-snp')",
"BP": "Base-pair coordinate (omitted with 'no-snp')",
"A1": "Allele 1 (omitted with 'no-snp')",
"A2": "Allele 2 (when present)",
"TEST": "Test identifier",
"NMISS": "Observations with nonmissing genotype, phenotype, and covariates",
"OR": "Odds ratio (without '--logistic beta')",
"BETA": "Log-odds coefficient ('--logistic beta')",
"SE": "Standard error of beta / log-odds (--ci)",
"L95": "Lower end of symmetric approx. CI for OR (--ci)",
"U95": "Upper end of symmetric approx. CI for OR (--ci)",
"STAT": "t-statistic",
"P": "Asymptotic p-value for t-statistic",
"CHISQ": "Chi-square (when reported for some tests)"
}
},
"regenie": {
"meta_data": {
"format_name": "regenie",
"format_source": "https://rgcgithub.github.io/regenie/",
"format_source_2": "https://github.com/rgcgithub/regenie/blob/master/example/test_bin_out_firth_Y1.regenie",
"format_version": "20220726",
"format_cite_name": "REGENIE",
"format_separator": " ",
"format_na": "NA",
"format_comment": null,
"format_col_order": [
"CHROM",
"GENPOS",
"ID",
"ALLELE0",
"ALLELE1",
"A1FREQ",
"N",
"TEST",
"BETA",
"SE",
"CHISQ",
"LOG10P"
],
"last_check_date": 20230501
},
"format_dict": {
"ID": "SNPID",
"CHROM": "CHR",
"GENPOS": "POS",
"ALLELE0": "NEA",
"ALLELE1": "EA",
"A1FREQ": "EAF",
"N": "N",
"INFO": "INFO",
"BETA": "BETA",
"SE": "SE",
"CHISQ": "CHISQ",
"LOG10P": "MLOG10P",
"TEST": null
}
},
"tensorqtl_cis_nominal": {
"meta_data": {
"format_name": "tensorqtl_cis_nominal",
"format_source": "https://raw.githubusercontent.com/broadinstitute/tensorqtl/refs/heads/master/docs/outputs.md",
"format_version": "20220726",
"format_cite_name": "tensorQTL",
"format_description": "tensorQTL cis-nominal mode output format"
},
"format_dict": {
"variant_id": "SNPID",
"phenotype_id": "TRAIT",
"start_distance": "START_DISTANCE",
"end_distance": "END_DISTANCE",
"af": "EAF",
"ma_samples": "MA_SAMPLES",
"ma_count": "MA_COUNT",
"pval_nominal": "P",
"slope": "BETA",
"slope_se": "SE"
},
"header_description": {
"phenotype_id": "Phenotype ID",
"variant_id": "Variant ID",
"start_distance": "Distance between the variant and phenotype start position (e.g., TSS)",
"end_distance": "Distance between the variant and phenotype end position (only present if different from start position)",
"af": "In-sample ALT allele frequency of the variant",
"ma_samples": "Number of samples carrying at least one minor allele",
"ma_count": "Number of minor alleles",
"pval_nominal": "Nominal p-value of the association between the phenotype and variant",
"slope": "Regression slope",
"slope_se": "Standard error of the regression slope"
}
},
"mtag": {
"meta_data": {
"format_name": "mtag",
"format_source": "https://github.com/JonJala/mtag/wiki/Tutorial-1:-The-Basics",
"format_version": "v1.0.8",
"format_separator": "\t",
"format_cite_name": "MTAG v1.0.8",
"format_comment": null,
"format_na": null,
"format_col_order": [
"snpid",
"chr",
"bpos",
"a1",
"a2",
"freq",
"beta",
"se",
"z",
"pval",
"p_value",
"n"
]
},
"format_dict": {
"snpid": "rsID",
"chr": "CHR",
"bpos": "POS",
"a2": "NEA",
"a1": "EA",
"freq": "EAF",
"n": "N",
"beta": "BETA",
"se": "SE",
"pval": "P",
"p_value": "P",
"z": "Z"
}
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"Pval_Estimate": "P",
"neg_log_10_p_value": "MLOG10P",
"MLOG10P": "MLOG10P",
"LOG10_P": "MLOG10P",
"LOG10P": "MLOG10P",
"chisq": "CHISQ",
"chisq_association": "CHISQ",
"CHISQ_BOLT_LMM": "CHISQ",
"Q": "Q",
"Q_df": "DOF",