I am trying to validate the variants I found using whole genome sequencing . The standard practice, I have seen in the two publications below were to check for the number of heterozygous SNPs called by the SNP array.
To further assess the accuracy of the variant calling, ... Of the 260,112 heterozygous calls detected with the Omni array, 99.5% were present in the entire SNV data set, 99.34% were concordant calls and only 0.16% were platform-specific SNVs. This demonstrates that both platforms are sensitive to known SNVs and that few known single-nucleotide polymorphisms (SNPs) are detected by only one platform.
To confirm that shared SNVs are indeed true variants, we used Illumina single-nucleotide polymorphism (SNP) arrays and selected all SNPs heterozygous on the SNP array.
My question is - why are only heterozygous SNPs chosen for validation when using Illumina Omni arrays?