GAWMerge, a protocol for integrating array and WGS data is shown in Fig. 1 and described in more detail in the Results. The WGS data were first prepared by extracting the selected control samples and the variants available within the array genotyping data. Utilizing the intersection of variants was important, as many false positives were introduced without this step13. This extraction of samples and variants was performed by BCFtools33. After QC, the intersection of SNPs between the array and WGS data was extracted, and the datasets were phased independently using SHAPEIT234,35. The datasets were then merged using BCFtools33.
