FormatBook — Format Summary

Generated 2026-08-03 05:38 UTC · 46 tool formats · tier coverage and parsing metadata

46
Formats
6.39
Avg tiers satisfied
9
Tier groups
46
Visible rows

Canonical header coverage

Tier satisfied Partial (all-mode: some headers missing) Not satisfied Click a format name to expand details Click column headers or Hide explanations to toggle header detail
Format
Variant ID
any · SNPID, rsID
At least one variant identifier column (SNPID or rsID).
Genomic location
all · CHR, POS
Both chromosome and base-pair position must be mapped.
Effect / other allele
all · EA, NEA
Both effect allele and non-effect allele must be mapped.
Effect size
any · BETA, OR, HR, Z
At least one effect-size statistic (beta, odds ratio, hazard ratio, or Z-score).
Uncertainty
any · SE
Standard error of the effect estimate.
P-value
any · P, MLOG10P
P-value or minus log10 p-value.
Sample size
any · N, N_CASE
Total sample size or case count (case-control studies may also map N_CONTROL separately).
Allele frequency
any · EAF, MAF, NEAF
Effect, minor, or non-effect allele frequency.
Imputation / QC
any · INFO
Imputation quality or INFO score.
 Tiers
.sample ○ ○ ○ ○ ○ ○ ○ ○ ○ 0/9
bgenie ● ● ● ● ● ● ○ ● ● 8/9
.stats ● ● ● ● ● ● ○ ● ● 8/9
CCGWAS ● ● ● ● ● ● ○ ○ ○ 6/9
cojo ● ○ ● ● ● ● ● ● ○ 7/9
fastgwa ● ● ● ● ● ● ○ ● ○ 7/9
gemma ● ● ● ● ● ● ○ ● ○ 7/9
genomicSEM ● ● ● ● ● ● ● ● ○ 8/9
gwascatalog ● ● ● ● ● ● ○ ● ○ 7/9
gwascatalog_hm ● ● ● ● ● ● ○ ● ○ 7/9
gwaslab ● ● ● ● ● ● ● ● ● 9/9
ldak ● ○ ● ● ● ○ ● ● ○ 6/9
ldsc ● ● ● ● ○ ● ● ● ● 8/9
MESuSiE ● ◐ ○ ● ● ○ ● ○ ○ 4/9
metal ● ○ ● ● ● ● ○ ● ○ 6/9
mrmega ● ● ● ○ ○ ● ● ● ○ 6/9
mtag ● ● ● ● ● ● ● ● ○ 8/9
pgscatalog ● ● ● ● ○ ○ ○ ● ○ 5/9
pgscatalog_hm Harmonized File ● ● ● ● ○ ○ ○ ● ○ 5/9
pheweb ● ● ● ● ● ● ● ● ● 9/9
plink1_assoc_outputs ● ● ● ● ● ● ● ● ● 9/9
plink2_glm_outputs ● ● ◐ ● ● ● ● ● ● 8/9
.glm.firth ● ● ◐ ● ● ● ● ● ● 8/9
.glm.linear ● ● ◐ ● ● ● ● ● ● 8/9
.glm.logistic ● ● ◐ ● ● ● ● ● ● 8/9
.assoc ● ● ● ● ● ● ○ ○ ○ 6/9
.bim ● ● ● ○ ○ ○ ○ ○ ○ 3/9
.assoc.dosage ● ● ● ● ● ● ○ ● ● 8/9
.fam ○ ○ ○ ○ ○ ○ ○ ○ ○ 0/9
.assoc.fisher ● ● ● ● ● ● ○ ○ ○ 6/9
.assoc.linear ● ● ● ● ● ● ● ○ ○ 7/9
.assoc.logistic ● ● ● ● ● ● ● ○ ○ 7/9
.psam ○ ○ ○ ○ ○ ○ ○ ○ ○ 0/9
.pvar ● ● ○ ○ ○ ○ ○ ○ ● 3/9
popcorn ● ○ ● ● ● ● ● ● ○ 7/9
regenie ● ● ● ● ● ● ● ● ● 9/9
regenie_gene ● ● ● ● ● ● ● ● ○ 8/9
saige ● ● ● ● ● ● ● ● ● 9/9
snptest ● ● ● ● ● ● ● ● ● 9/9
ssf ● ● ● ● ● ● ● ● ● 9/9
tensorqtl_cis ● ○ ○ ● ● ● ○ ● ○ 5/9
tensorqtl_cis_independent ● ○ ○ ● ● ● ○ ● ○ 5/9
tensorqtl_cis_nominal ● ○ ○ ● ● ● ○ ● ○ 5/9
tensorqtl_cis_nominal_interaction ● ○ ○ ○ ○ ○ ○ ● ○ 2/9
tensorqtl_trans ● ○ ○ ● ● ● ○ ● ○ 5/9
vcf ● ● ● ● ● ● ● ● ● 9/9

Format metadata

Striped rows alternate formats; gray cells are unset metadata. Click a value to expand or collapse long text. Click Copy in the Citation column to copy the full reference.

Format
Separator
Field delimiter between columns (e.g. TAB, SPACE).
NA value
Token(s) used for missing values.
Comment
Prefix character marking comment lines.
Header row
Whether the file includes a header row.
Header lines
Number of header lines before data rows.
Cite name
Short software or format name for citations.
Citation
Copy the full citation string to the clipboard.
Version
Format specification or software version.
Last check
Date the format spec was last verified.
.sample SPACE NA — yes 2 Oxford/BGEN 20260208 20260208
bgenie SPACE — 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). — — BGENIE latest —
.stats — — — — — BOLT-LMM v2.4 (July 22, 2022) —
CCGWAS TAB — — — — CC-GWAS 20220901 20250416
cojo — — — — — GCTA-COJO 20230807 —
fastgwa — — — — — fastGWA 20220726 —
gemma TAB — GEMMA univariate linear mixed model (LMM) output format. Columns: chr, rs, ps, n_miss, allele1, allele0, af, beta, se, l_remle, p_wald. The output is tab-separated. allele1 is the effect allele, allele0 is the non-effect allele, af is the allele frequency of allele1, and l_remle is the log-likelihood ratio test statistic. — — GEMMA 0.98.5 —
genomicSEM — — — — — genomicSEM 20241210 —
gwascatalog — — — — — GWAS Catalog 20220726 —
gwascatalog_hm — — — — — GWAS Catalog 20220806 —
gwaslab TAB — — yes — GWASLab v4.0.5 20260109
ldak TAB — — yes — LDAK/SumHer 20260801 20260801
ldsc — — — — — LDSC 20150306 —
MESuSiE — — — — — MESuSiE 20221109 —
metal — — — — — METAL 20220726 —
mrmega — — — — — MR-MEGA ver0.2 20220806
mtag TAB — — — — MTAG v1.0.8 v1.0.8 —
pgscatalog — — — — — PGS Catalog 20220726 —
pgscatalog_hm Harmonized File — — — — — PGS Catalog 20220726 —
pheweb 'tab, space, or comma' , ., NA, N/A, n/a, nan, -nan, NaN, -NaN, null, NULL — yes — PheWeb 20220928 20250106
plink1_assoc_outputs TAB — — yes — PLINK 1.9 PLINK 1.9 (doc revision 19 Aug 2025) 20260326
plink2_glm_outputs TAB . # yes — PLINK 2.0 PLINK 2.0 (doc revision 11 Mar 2026) 20260326
.glm.firth TAB . # yes — PLINK 2.0 PLINK 2.0 (doc revision 11 Mar 2026) 20260326
.glm.linear TAB . # yes — PLINK 2.0 PLINK 2.0 (doc revision 11 Mar 2026) 20260326
.glm.logistic TAB . # yes — PLINK 2.0 PLINK 2.0 (doc revision 11 Mar 2026) 20260326
.assoc TAB — — yes — PLINK 1.9 PLINK 1.9 (doc revision 19 Aug 2025) 20260326
.bim TAB — — no — PLINK 1.9 PLINK 1.9 (doc revision 19 Aug 2025) 20260326
.assoc.dosage TAB — — yes — PLINK 1.9 PLINK 1.9 (doc revision 19 Aug 2025) 20260326
.fam TAB — — no — PLINK 1.9 PLINK 1.9 (doc revision 19 Aug 2025) 20260326
.assoc.fisher TAB — — yes — PLINK 1.9 PLINK 1.9 (doc revision 19 Aug 2025) 20260326
.assoc.linear TAB — — yes — PLINK 1.9 PLINK 1.9 (doc revision 19 Aug 2025) 20260326
.assoc.logistic TAB — — yes — PLINK 1.9 PLINK 1.9 (doc revision 19 Aug 2025) 20260326
.psam TAB NA # yes — PLINK 2.0 PLINK 2.0 (doc revision 11 Mar 2026) 20260326
.pvar TAB . # yes — PLINK 2.0 PLINK 2.0 (doc revision 11 Mar 2026) 20260326
popcorn — — — — — Popcorn 20230807 —
regenie SPACE NA — — — REGENIE 20220726 20230501
regenie_gene SPACE NA # — — REGENIE 20230926 20230926
saige — — — — — SAIGE v1.1.3 20220806
snptest — — — — — SNPTEST v2.5.4-beta3 —
ssf TAB #NA — — — GWAS-SSF v0.1 20230328 —
tensorqtl_cis — — — — — tensorQTL 20220726 —
tensorqtl_cis_independent — — — — — tensorQTL 20220726 —
tensorqtl_cis_nominal — — — — — tensorQTL 20220726 —
tensorqtl_cis_nominal_interaction — — — — — tensorQTL 20220726 —
tensorqtl_trans — — — — — tensorQTL 20220726 —
vcf — — — — — GWAS-VCF 20220923 —