Fig. 2.

The general steps used to filter variants from WES. The approximate number of variants in each step is indicated. All filtering steps can be applied in silico. The number of variants that remain after filtering depends on the cut-off values used for filtering based on allele frequency and on algorithms used to call CNVs [3, 19, 26]. CNV numbers are highly dependent on the algorithm used; therefore, the number of CNVs is not indicated here. For the analysis of de novo variants, sequencing of a patient’s parents as a trio is required, after which all variants present in the parents can be filtered [3].