ABSTRACT
A key insight was the understanding that the size of the mutational target is related to the population frequency of genetic diseases that are largely caused by de novo mutations. For instance, de novo mutations in the SET-binding protein 1 (SETBP1) cause Schinzel–Giedion syndrome, a rare disorder characterized by severe mental retardation, distinctive facial features and multiple congenital malformations. This chapter shows how to perform de novo variant calling using a simple heuristic and then reviews a more sophisticated approach. To start with, one needs to generate a joint Variant Call Format (VCF) file from all three samples from a trio. Joint calling is the most straightforward way of doing it. With joint calling, Genome Analysis Toolkit (GATK) generates a single call set for all analyzed samples. The chapter presents a simple filter derived from recommendations made in the course of a project that sequenced 10 Danish trios at high depth in order to estimate the de novo mutation rate.
