This application was designed to check the allele frequency in the summary data file by comparing the allele frequencies in the uploaded dataset to those in the 1000 Genomes superpopulation. The presence of SNPs with allele frequency > 0.5 in the uploaded dataset implies an allele frequency conflict. If the majority of SNPs in the GWAS summary stats have allele frequency conflict, it is recommended not using for the downstream Mendelian randomization analysis.
This application uses packages mainly from:
Design and quality control of large-scale two-sample Mendelian randomization studies
doi: https://doi.org/10.1101/2021.07.30.21260578
For more information, please visit the following links:
Special thanks to the developers of the R packages used in this application.