genomicSEM
Overview
| Field |
Value |
| Format key |
genomicsem |
| Spec file |
formats/genomicsem.json |
| Cite name |
genomicSEM |
| Version |
20241210 |
| Source |
https://github.com/GenomicSEM/GenomicSEM/wiki/4.-Common-Factor-GWAS |
| Source (2) |
https://github.com/GenomicSEM/GenomicSEM/wiki/5.-Multivariate-GWAS |
| GitHub |
https://github.com/GenomicSEM/GenomicSEM |
| Citation |
Grotzinger, A. D., Rhemtulla, M., de Vlaming, R., Ritchie, S. J., Mallard, T. T., Hill, W. D., ... & Tucker-Drob, E. M. (2019). Genomic structural equation modelling provides insights into the multivariate genetic architecture of complex traits. Nature communications, 10(1), 3402. |
| ## Column mapping |
|
| Raw header |
Canonical |
Canonical (secondary) |
A1 |
EA |
— |
A2 |
NEA |
— |
BP |
POS |
— |
CHR |
CHR |
— |
est |
BETA |
— |
Frq |
EAF |
— |
MAF |
MAF |
— |
N |
N |
— |
Pval_Estimate |
P |
— |
Q |
Q |
— |
Q_df |
DOF |
— |
Q_pval |
P_HET |
— |
se_c |
SE |
— |
SNP |
SNPID |
rsID |
Z_Estimate |
Z |
— |
| ## 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, Z |
OR, HR |
| Uncertainty |
yes |
SE |
— |
| P-value |
yes |
P |
MLOG10P |
| Sample size |
yes |
N |
N_CASE |
| Allele frequency |
yes |
EAF, MAF |
NEAF |
| Imputation / QC |
no |
— |
INFO |
| ## See also |
|
|
|