Upload GWAS Analysis Files

1. GeneWeaver IDs *

Enter GeneWeaver database IDs separated by commas

Important: Do not add spaces between commas

Example format: 399058,399061,1777 (no spaces)

2. GeneWeaver Labels *

Enter descriptive names for each GeneWeaver ID

Important: Use underscores instead of spaces

Example: For IDs 75605,407736 use labels: Alcoholic_Frontal_Cortex,Alcohol_Gene_Expression_Mice

3. GWAS Summary Statistics File *

Upload your GWAS results in compressed .gz format

Need an example? Download: DPW.gz

File must be compressed as .gz

4. GWAS Sample Size *

Total number of individuals in your study

Example: If your study had 50,000 participants, enter: 50000

5. Window Size (Buffer Region) *

Distance around genes to include variants

Range: 100 to 100,000 base pairs

Common values: 10000 (10Kb), 50000 (50Kb), 100000 (100Kb)

6. Target BIM File (Optional)

Note: If you want to compute the PGS for each geneset or union geneset, you must provide a target BIM file that contains only HapMap variants (please see the details on how to subset the HapMap variants from the PLINK file).

If you do not want to compute the PGS, you can skip uploading the BIM file

⚠️ Important Notice

By uploading your data, you agree that the BGA Laboratory may use CONSILIENCE-GWAS for analysis. Your data will remain private and confidential and will be automatically deleted within 10 days.

📋 File Format Requirements

Required Columns

Your GWAS file must include these 8 columns (in exact order):

Column	Description	Example
SNP_ID	Variant identifier (rs number)	rs11130222
CHR	Chromosome number (1-22)	3
POS	Genomic position	49901060
A1	Effect allele	A
A2	Other allele	T
Beta	Effect size	0.026
SE	Standard error	0.003
Pval	P-value	4.581e-25

📝 File Preparation Tips

✓ File format: Must be compressed as .gz file
✓ Header: First line must contain exactly these column names
⚠ Missing positions: If your file lacks chromosome/position, use Map_RSID tool
⚠ Z-scores: Convert Z-scores to Beta/SE using this guide

🗜️ How to Compress Your File

Using R:

# Save your data as a .gz file
library(R.utils)
write.table(your_data, "yourfile.txt", sep="\t", row.names=FALSE, col.names=TRUE, quote=FALSE)
gzip("yourfile.txt", destname="yourfile.gz", overwrite=TRUE)

Using Windows:

Right-click file → 7-Zip → Add to archive → Select .gz format