ABSTRACT
Quality control (QC) of the number and distribution of called variants is one of the important quality control steps in WES/WGS analysis. There are a number of QC packages available that can be used to calculate the following metrics, including QC3 and bcftools stats. This chapter illustrates how to calculate the metrics using command-line tools in the exercises so that readers can gain some intuition. The Ti/Tv ratio is a commonly used quality control parameter for the distribution of variants in exome and genome datasets. It is computed as the number of transition single-nucleotide variants (SNVs) divided by the number of transversion SNVs. The total number of variants, as well as the number of novel variants, will vary from sample to sample and may be related to the populations background of the individual being sequenced. Many of the variants common to these populations may not be in the databases and be interpreted as novel.
