Fig. 2From: Transfer learning for genotype–phenotype prediction using deep learning modelsModule 3: Plot linkage disequilibrium, manhattan, and QQplot. Genotype data generated from PS is passed to Gtool -> Plink to convert genotype data into VCF file format, and that file is used to generate linkage disequilibrium. Gtool output is also used to find p-values for each SNP and generate the manhattan plotBack to article page