bgenie¶
Overview¶
| Field | Value |
|---|---|
| Format key | bgenie |
| Spec file | formats/bgenie.json |
| Cite name | BGENIE |
| Version | latest |
| Source | https://jmarchini.org/bgenie/ |
| Citation | Bycroft, C., Freeman, C., Petkova, D., Band, G., Elliott, L. T., Sharp, K., Motyer, A., Vukcevic, D., Delaneau, O., O'Connell, J., Cortes, A., Welsh, S., McVean, G., Leslie, S., Donnelly, P., & Marchini, J. (2018). The UK Biobank resource with deep phenotyping and genomic data. Nature, 562(7726), 203-209. |
| ## File layout |
| Field | Value |
|---|---|
| Separator | SPACE |
| Comment prefix | 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). |
| ## Column mapping |
| Raw header | Canonical |
|---|---|
a_0 |
NEA |
a_1 |
EA |
af |
EAF |
chr |
CHR |
info |
INFO |
pheno1_beta |
BETA |
pheno1_p |
MLOG10P |
pheno1_se |
SE |
pheno1_t |
T |
pos |
POS |
rsid |
rsID |
| ## Coverage |
8/9 tier groups satisfied.
| Tier | Status | Matched | Missing |
|---|---|---|---|
| Variant ID | yes | rsID | SNPID |
| Genomic location | yes | CHR, POS | — |
| Effect / other allele | yes | EA, NEA | — |
| Effect size | yes | BETA | OR, HR, Z |
| Uncertainty | yes | SE | — |
| P-value | yes | MLOG10P | P |
| Sample size | no | — | N, N_CASE |
| Allele frequency | yes | EAF | MAF, NEAF |
| Imputation / QC | yes | INFO | — |
| ## See also |