.fam
Per-sample row for .bed: FID, IID, father IID, mother IID, sex, phenotype. Quantitative phenotype if numeric values other than {-9,0,1,2} appear.
Overview
| Field |
Value |
| Format key |
plink_fam |
| Spec file |
formats/plink_fam.json |
| Cite name |
PLINK 1.9 |
| Version |
PLINK 1.9 (doc revision 19 Aug 2025) |
| Last checked |
20260326 |
| Source |
https://www.cog-genomics.org/plink/1.9/formats#fam |
| Citation |
Purcell, S., Neale, B., Todd-Brown, K., Thomas, L., Ferreira, M. A., Bender, D., ... & Sham, P. C. (2007). PLINK: a tool set for whole-genome association and population-based linkage analyses. The American journal of human genetics, 81(3), 559-575. |
| ## File layout |
|
| Field |
Value |
| Separator |
TAB |
| Header row |
no |
| Column order |
0, 1, 2, 3, 4, 5 |
| ## Column mapping |
|
| Raw header |
Canonical |
0 |
FID |
1 |
IID |
2 |
PAT |
3 |
MAT |
4 |
SEX |
5 |
PHENO1 |
| ## Header descriptions |
|
| Column |
Description |
0 |
Family ID |
1 |
Within-family ID (cannot be '0') |
2 |
Paternal IID ('0' if unknown) |
3 |
Maternal IID ('0' if unknown) |
4 |
Sex (1=male, 2=female, 0=unknown) |
5 |
Phenotype (1=control, 2=case; -9/0/non-numeric missing for case/control) |
| ## Coverage |
|
0/9 tier groups satisfied.
| Tier |
Status |
Matched |
Missing |
| Variant ID |
no |
— |
SNPID, rsID |
| Genomic location |
no |
— |
CHR, POS |
| Effect / other allele |
no |
— |
EA, NEA |
| Effect size |
no |
— |
BETA, OR, HR, Z |
| Uncertainty |
no |
— |
SE |
| P-value |
no |
— |
P, MLOG10P |
| Sample size |
no |
— |
N, N_CASE |
| Allele frequency |
no |
— |
EAF, MAF, NEAF |
| Imputation / QC |
no |
— |
INFO |
| ## See also |
|
|
|