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We established a bioinformatics procedure at our laboratory that processes sequencing data, identifies single nucleotide variants (SNVs) and small insertions/deletions (indels), annotates the variants based on the curated variant databases and algorithms, and filters variants according to custom defined filtration schemas that are selected by geneticists specifically for each case. Since we are operating in the clinical settings, rigorous validation procedures are applied at each step to ensure the accuracy and quality of the data. Here we describe how we implemented our current clinical exome pipeline, and our approaches for validation.