Summary Statistics
GWASStudio requires summary-statistics files(s) to be harmonized and formatted in tsv.gz.
Core Summary Statistics columns
| Column | Description |
|---|---|
CHR |
Chromomsome in integer format |
POS |
Position of the variant |
EA |
Effect allele |
NEA |
Non-effect alle |
EAF |
Effect allele frequency |
BETA |
Effect size |
SE |
Standard error |
Additional optional columns
| Column | Description |
|---|---|
Z |
Z-score |
MLOG10P |
p-value in -log10 format |
rsID |
SNP ID following dbSNP convention |
SNPID |
SNPID described as CHR:POS:A1:A2 with A1 and A2 being the alleles in alphabetical order |
N |
Sample size |
STATUS |
Sample size |
Note
To harmonize and format data in the appropriate way, please refer to the harmonization_pipeline.