regenie_gene
Overview
| Field |
Value |
| Format key |
regenie_gene |
| Spec file |
formats/regenie_gene.json |
| Cite name |
REGENIE |
| Version |
20230926 |
| Last checked |
20230926 |
| Source |
https://rgcgithub.github.io/regenie/ |
| Source (2) |
https://github.com/rgcgithub/regenie/blob/master/example/test_bin_out_firth_Y1.regenie |
| GitHub |
https://github.com/rgcgithub/regenie |
| Citation |
Mbatchou, J., Barnard, L., Backman, J., Marcketta, A., Kosmicki, J. A., Ziyatdinov, A., ... & Marchini, J. (2021). Computationally efficient whole-genome regression for quantitative and binary traits. Nature genetics, 53(7), 1097-1103. |
| ## File layout |
|
| Field |
Value |
| Separator |
SPACE |
| NA value |
NA |
| Comment prefix |
# |
| Column order |
CHROM, GENPOS, ID, ALLELE0, ALLELE1, A1FREQ, N, TEST, BETA, SE, CHISQ, LOG10P |
| ## Column mapping |
|
| Raw header |
Canonical |
A1FREQ |
EAF |
ALLELE0 |
NEA |
ALLELE1 |
EA |
BETA |
BETA |
CHISQ |
CHISQ |
CHROM |
CHR |
EXTRA |
DOF |
GENPOS |
POS |
ID |
SNPID |
LOG10P |
MLOG10P |
N |
N |
SE |
SE |
TEST |
TEST |
| ## Coverage |
|
8/9 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 |
MLOG10P |
P |
| Sample size |
yes |
N |
N_CASE |
| Allele frequency |
yes |
EAF |
MAF, NEAF |
| Imputation / QC |
no |
— |
INFO |
| ## See also |
|
|
|