Subtracting the unaffected child's genome

We can use the unaffected child's genome to further filter the SNPs. Any SNPs found homozygous in this child are not the disease SNPs. The child may be a carrier but we don't know. First select the homozygous SNPs as before. This step is not shown but the results are in the history panel below as dataset twenty-three.

To filter the results, this time we will be using Subtract (red arrow) instead of Intersect. We want to Subtract NA12882 - son homozygous from the Homozygous in affected and heterozygous in parents dataset. We want intervals or SNPs with no overlap, where minimal overlap is defined as one base. Click the Execute button (green arrow).