.glm.logistic¶
Logistic or Firth logistic from --glm (case/control). LOG(OR)_SE is SE on log-odds scale; Z_STAT is Wald Z. Column set varies with cols= and case/control count columns.
Overview¶
| Field | Value |
|---|---|
| Format key | plink2_logistic |
| Spec file | formats/plink2_logistic.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#glm_logistic |
| 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 order | #CHROM, POS, ID, REF, ALT1, ALT, PROVISIONAL_REF?, A1, OMITTED, A1_CT, ALLELE_CT, A1_CASE_CT, A1_CTRL_CT, CASE_ALLELE_CT, CTRL_ALLELE_CT, CASE_NON_A1_CT, CASE_HET_A1_CT, CASE_HOM_A1_CT, CTRL_NON_A1_CT, CTRL_HET_A1_CT, CTRL_HOM_A1_CT, A1_FREQ, A1_CASE_FREQ, A1_CTRL_FREQ, MACH_R2, FIRTH?, TEST, OBS_CT, BETA, OR, LOG(OR)_SE, L95, U95, Z_STAT, F_STAT, P, ERRCODE, LOG10_P |
| ## Column mapping |
| Raw header | Canonical | Canonical (secondary) |
|---|---|---|
#CHROM |
CHR | — |
A1 |
EA | — |
A1_CASE_CT |
— | — |
A1_CASE_FREQ |
EAF_CASE | — |
A1_CT |
— | — |
A1_CTRL_CT |
— | — |
A1_CTRL_FREQ |
EAF_CONTROL | — |
A1_FREQ |
EAF | — |
ALLELE_CT |
— | — |
ALT |
ALT | — |
ALT1 |
— | — |
BETA |
BETA | — |
CASE_ALLELE_CT |
— | — |
CASE_HET_A1_CT |
— | — |
CASE_HOM_A1_CT |
— | — |
CASE_NON_A1_CT |
— | — |
CHROM |
CHR | — |
CTRL_ALLELE_CT |
— | — |
CTRL_HET_A1_CT |
— | — |
CTRL_HOM_A1_CT |
— | — |
CTRL_NON_A1_CT |
— | — |
ERRCODE |
— | — |
F_STAT |
F | — |
FIRTH? |
— | — |
ID |
SNPID | rsID |
L95 |
OR_95L | — |
LOG(OR)_SE |
SE | — |
LOG10_P |
MLOG10P | — |
MACH_R2 |
INFO | — |
OBS_CT |
N | — |
OMITTED |
— | — |
OR |
OR | — |
P |
P | — |
POS |
POS | — |
PROVISIONAL_REF? |
— | — |
REF |
REF | — |
SE |
SE | — |
TEST |
— | — |
U95 |
OR_95U | — |
Z_STAT |
Z | — |
| ## Header descriptions |
| Column | Description |
|---|---|
#CHROM |
Chromosome code |
A1 |
Counted allele in regression |
A1_CASE_FREQ |
A1 frequency in cases |
A1_CTRL_FREQ |
A1 frequency in controls |
A1_FREQ |
A1 allele frequency |
ALT |
All alternate alleles (comma-separated) |
ALT1 |
First alternate allele |
BETA |
Log-odds coefficient for A1 |
ERRCODE |
Reason for NA result |
F_STAT |
F-statistic (joint tests) |
FIRTH? |
Whether Firth regression was used |
ID |
Variant ID |
L95 |
Lower symmetric approx. CI for OR (--ci) |
LOG(OR)_SE |
Standard error of log-odds (beta) |
LOG10_P |
Optional -log10(p) column |
MACH_R2 |
MaCH imputation R-squared |
OBS_CT |
Samples in regression |
OMITTED |
Omitted allele |
OR |
Odds ratio for A1 |
P |
Asymptotic p-value |
POS |
Base-pair coordinate |
PROVISIONAL_REF? |
Whether REF is provisional |
REF |
Reference allele |
TEST |
Test identifier |
U95 |
Upper symmetric approx. CI for OR (--ci) |
Z_STAT |
Wald Z-score |
| ## 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 |