Finding SNPs heterozygous in both parents

For the affected children to be homozygous they must have inherited the disease allele from both of the parents. So both must have the same heterozygous allele. A simple intersection of the two heterozygous datasets will give us this filtered set. As the blue arrow shows there are still over two million SNPs before the intersection.

This operation is based on genomic coordinates so we will open the section Operate on Genomic Intervals, and use the Intersect tool (red arrow). We want the overlapping intervals in the parents filtered SNPs. One base overlap is all we need as these are SNPs are only one base long. Click the Execute button (green arrow).