saige
Overview
| Field |
Value |
| Format key |
saige |
| Spec file |
formats/saige.json |
| Cite name |
SAIGE |
| Version |
v1.1.3 |
| Last checked |
20220806 |
| Source |
https://saigegit.github.io/SAIGE-doc/docs/single_step2.html |
| GitHub |
https://github.com/weizhouUMICH/SAIGE |
| Citation |
Zhou, W., Nielsen, J. B., Fritsche, L. G., Dey, R., Gabrielsen, M. E., Wolford, B. N., ... & Lee, S. (2018). Efficiently controlling for case-control imbalance and sample relatedness in large-scale genetic association studies. Nature genetics, 50(9), 1335-1341. |
| ## Column mapping |
|
| Raw header |
Canonical |
AF_Allele2 |
EAF |
Allele1 |
NEA |
Allele2 |
EA |
BETA |
BETA |
CHR |
CHR |
imputationInfo |
INFO |
N |
N |
p.value |
P |
POS |
POS |
SE |
SE |
SNPID |
SNPID |
| ## Coverage |
|
9/9 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 |
P |
MLOG10P |
| Sample size |
yes |
N |
N_CASE |
| Allele frequency |
yes |
EAF |
MAF, NEAF |
| Imputation / QC |
yes |
INFO |
— |
| ## See also |
|
|
|