ssf
Overview
| Field |
Value |
| Format key |
ssf |
| Spec file |
formats/ssf.json |
| Cite name |
GWAS-SSF v0.1 |
| Version |
20230328 |
| Source |
https://www.ebi.ac.uk/gwas/docs/summary-statistics-format |
| Citation |
Hayhurst, J., Buniello, A., Harris, L., Mosaku, A., Chang, C., Gignoux, C. R., ... & Barroso, I. (2022). A community driven GWAS summary statistics standard. bioRxiv. |
| ## File layout |
|
| Field |
Value |
| Separator |
TAB |
| NA value |
#NA |
| Column order |
chromosome, base_pair_location, effect_allele, other_allele, beta, odds_ratio, hazard_ratio, standard_error, effect_allele_frequency, p_value, neg_log_10_p_value, ci_upper, ci_lower, rsid, variant_id, info, ref_allele, n |
| ## Column mapping |
|
| Raw header |
Canonical |
base_pair_location |
POS |
beta |
BETA |
chromosome |
CHR |
ci_lower |
OR_95L |
ci_upper |
OR_95U |
effect_allele |
EA |
effect_allele_frequency |
EAF |
hazard_ratio |
HR |
info |
INFO |
n |
N |
neg_log_10_p_value |
MLOG10P |
odds_ratio |
OR |
other_allele |
NEA |
p_value |
P |
ref_allele |
REF |
rsid |
rsID |
standard_error |
SE |
variant_id |
SNPID |
| ## Coverage |
|
9/9 tier groups satisfied.
| Tier |
Status |
Matched |
Missing |
| Variant ID |
yes |
SNPID, rsID |
— |
| Genomic location |
yes |
CHR, POS |
— |
| Effect / other allele |
yes |
EA, NEA |
— |
| Effect size |
yes |
BETA, OR, HR |
Z |
| Uncertainty |
yes |
SE |
— |
| P-value |
yes |
P, MLOG10P |
— |
| Sample size |
yes |
N |
N_CASE |
| Allele frequency |
yes |
EAF |
MAF, NEAF |
| Imputation / QC |
yes |
INFO |
— |
| ## See also |
|
|
|