Figure 1

Study design and GACT functionality. The left side of the figure indicates that microarray data can be used to call SNPs in any of the four listed SNP definitions. Often, when genotypes are obtained from public repositories (e.g. dbGaP), allele definitions may not be immediately known to investigators. GACT will predict allele definition and genome build, and convert to any new definitions or builds. Since the SNP definition in the NGS data is determined during alignment to the human reference genome (Plus is a commonly-used definition), the SNP alleles from genotyping microarrays can be converted and matched to those from NGS. After GACT’s conversion, imputation, meta-analysis and (or) other analyses may be carried out using the commonly-used tools such as GWAMA, METAL, PLINK, and IMPUTE2.