An alteration in copy number state with respect to a single-copy reference locus is referred to as a “copy number variation” (CNV) if it appears in germline cells, or a copy number alteration (CNA) if it appears in somatic cells. A CNV or CNA could be due to a deletion or amplification of a locus with respect to the number of copies of the reference locus present in the cell, and together, they are major contributors to variability in the human genome. They have been associated with cancers; neurological, psychiatric, and autoimmune diseases; and adverse drug reactions. However, it is difficult to measure these allelic variations with high precision using other methods such as qPCR, thus making phenotypic and disease associations with altered CNV status challenging.