plink2_glm_outputs
Union of columns across .glm.linear, .glm.logistic, and .glm.firth; full column sets are in formats/plink2_*.json.
Overview
| Field |
Value |
| Format key |
plink2 |
| Spec file |
formats/plink2.json |
| Cite name |
PLINK 2.0 |
| Version |
PLINK 2.0 (doc revision 11 Mar 2026) |
| Last checked |
20260326 |
| Source |
https://www.cog-genomics.org/plink/2.0/formats |
| Citation |
Chang, C. C., Chow, C. C., Tellier, L. C., Vattikuti, S., Purcell, S. M., & Lee, J. J. (2015). Second-generation PLINK: rising to the challenge of larger and richer datasets. Gigascience, 4(1), s13742-015. |
| ## File layout |
|
| Field |
Value |
| Separator |
TAB |
| NA value |
. |
| Comment prefix |
# |
| Header row |
yes |
| ## Column mapping |
|
| Raw header |
Canonical |
Canonical (secondary) |
#CHROM |
CHR |
— |
A1 |
EA |
— |
A1_CASE_FREQ |
EAF_CASE |
— |
A1_CTRL_FREQ |
EAF_CONTROL |
— |
A1_FREQ |
EAF |
— |
ALT |
ALT |
— |
BETA |
BETA |
— |
CHROM |
CHR |
— |
F_STAT |
F |
— |
ID |
SNPID |
rsID |
L95 |
OR_95L |
— |
LOG(OR)_SE |
SE |
— |
LOG10_P |
MLOG10P |
— |
MACH_R2 |
INFO |
— |
OBS_CT |
N |
— |
OR |
OR |
— |
P |
P |
— |
POS |
POS |
— |
REF |
REF |
— |
SE |
SE |
— |
T_STAT |
T |
— |
U95 |
OR_95U |
— |
Z_STAT |
Z |
— |
| ## Coverage |
|
|
8/9 tier groups satisfied.
| Tier |
Status |
Matched |
Missing |
| Variant ID |
yes |
SNPID, rsID |
— |
| Genomic location |
yes |
CHR, POS |
— |
| Effect / other allele |
partial |
EA |
NEA |
| Effect size |
yes |
BETA, OR, Z |
HR |
| 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 |
|
|
|