ABSTRACT
Depth and coverage are two key parameters by which to judge the quality of a sequencing run and the read analysis. An assessment of these parameters makes up the second key step in WES/WGS quality control (Q/C). Capture efficiency is one of the most important quality control parameters for exome sequencing or other targeted sequencing (i.e., the percentage of reads that map to one of the targeted regions, sometimes called "on-target ratio"). The chapter shows how to perform coverage analysis using the NA12878 exome. This exome was enriched with the Nextera Rapid Capture Exome and Expanded Exome kit. BEDTools coverage computes both the depth and breadth of coverage of features (target regions) in the BED file with the features (reads) in the BAM file. The browser extensible data (BED) format provides a flexible way to define the data lines that are displayed in an annotation track.
