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gemma

Overview

Field Value
Format key gemma
Spec file formats/gemma.json
Cite name GEMMA
Version 0.98.5
Source https://github.com/genetics-statistics/GEMMA
GitHub https://github.com/genetics-statistics/GEMMA
Citation Zhou, X., & Stephens, M. (2012). Genome-wide efficient mixed-model analysis for association studies. Nature Genetics, 44(7), 821-824.
## File layout
Field Value
Separator TAB
Comment prefix GEMMA univariate linear mixed model (LMM) output format. Columns: chr, rs, ps, n_miss, allele1, allele0, af, beta, se, l_remle, p_wald. The output is tab-separated. allele1 is the effect allele, allele0 is the non-effect allele, af is the allele frequency of allele1, and l_remle is the log-likelihood ratio test statistic.
## Column mapping
Raw header Canonical
af EAF
allele0 NEA
allele1 EA
beta BETA
chr CHR
l_remle L_REMLE
n_miss N_MISS
p_wald P
ps POS
rs rsID
se SE
## Coverage

7/9 tier groups satisfied.

Tier Status Matched Missing
Variant ID yes rsID SNPID
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 no — N, N_CASE
Allele frequency yes EAF MAF, NEAF
Imputation / QC no — INFO
## See also