ABSTRACT
The Integrative Genomics Viewer (IGV) is a visualization tool for interactive exploration of large, integrated genomic datasets. This chapter demonstrates how to use IGV to view alignments and small variants in the NA12878 exome. IGV is a really nice piece of software with lots of bells and whistles. The chapter presents a small subset of these capabilities that are relevant to the analysis of small variants in exome sequencing. IGV can be used to view alignments in SAM or BAM format. In both cases, the alignment file needs to be indexed. IGV offers many reference genomes by default, so that users can choose a genome by clicking on it in the Genomes drop-down menu. It is a good idea to inspect any variants considered to be candidates for the experimental or medical workup in IGV to identify potential false-positive (poor-quality) variants early.
