Removing SNPs found in healthy individuals

Now we are ready to remove the "benign" SNPs from our input. In the tool panel, open the section called Operate on Genomic Intervals. (These are examples of tools that cannot be run on a masterVar file; they only work with "interval" formats, which includes pgSnp.) Click on Subtract (red arrow) to see the options for that tool in the center panel. We want to remove the SNPs that were found in the 24 genomes from our converted set (red arrows). Then click Execute (green arrow).

If we had not used a Complete Genomics dataset as our starting point, the next step would be to repeat the subtraction using the result from the first subtraction and the CG dataset brought in from the library.