Analysis Process
- Converts the input data to the format required by the GCTA software.
- Utilizes GCTA software COJO function to remove significant SNPs in the “GWAs” analysis
- Analyze whether any SNPs are still significant.
- Visualizes the results of the analysis.
Input and Output
Input Parameters
| Parameter | Description |
|---|---|
| Upload GWAs Data File | The .mlma file from the “GWAs” analysis. |
| Upload VCF Data File | The VCF data, format is shown in “Data Preparation”. |
| Threshold | A value setting the significance threshold (P-value) for COJO analysis. SNPs with P-values below this threshold are retained. Supports numeric input, defaulting to 5e-8. For users unsure of the significance threshold, entering “Bonferroni” sets it to 0.05 divided by the number of SNPs. |
| Color | Sets adjacent chromosome colors in the Manhattan plot. Hexadecimal colors are connected by “_” |
| Show Top SNPs | Whether to show the top SNPs in the Manhattan plot. |
| Other Parameters | Other parameters of the main invoked software for this analysis. |
Output Results
| Filename | Description |
|---|---|
| Time_GWAs_cojoed.log&.jma.cojo&.ldr.cojo&.cma.cojo | The output of the invoked software for the COJO analysis. |
| Time_GWAs_cojoedmanhattan.pdf&png | The visualized results of the COJO analysis. Includes a Manhattan plot of the association results. |
| Time_GWAs_cojoedtop_snps.txt | The association result of the top SNPs. |
| Time_GWAs_cojoedqqplot.pdf&png | The visualized results of the COJO analysis. Includes a QQ plot of the association results and a regression line of inflation factor. |
Citation
Yang, J., Ferreira, T., Morris, A.P., Medland, S.E., Madden, P.A.F., et al., 2012. Conditional and joint multiple-SNP analysis of GWAS summary statistics identifies additional variants influencing complex traits. Nat. Genet. 44, 369–375. https://doi.org/10.1038/ng.2213