A Bioinformatics Pipeline for Whole Exome Sequencing: Overview of the Processing and Steps from Raw Data to Downstream Analysis

Background

Next Generation Sequencing (NGS) technologies have paved the way for rapid sequencing efforts to analyze a wide number of samples. From the whole genome to transcriptome to exome, it has changed the way we look at nonspecific germline variants, somatic mutations, structural variant besides identifying associations between a variant and human genetic disease (Singleton et al., 2011). This can help understand the complex genetic disorders to get better diagnosis and assess disease risk. The analysis of exome sequencing data to find variants, however still poses multiple challenges. For example, there are several commercial and open source pipelines but configuring (Pabinger et al., 2014; Guo et al., 2015) them in terms of benchmarking and optimizing them is a time-consuming process. Among the steps, viz. quality check, alignment, recalibration, variant calling, variant annotation, one needs to reach consensus on the set of tools following which one’s output should be fed as other tool’s input (Stajich et al., 2002; Gentleman et al., 2004; Chang and Wang, 2012). While integrating, it would be appropriate to check and use the tools before reproducing and maintaining highly heterogeneous pipelines (Hwang et al., 2015). In this protocol, we discuss the steps for whole exome sequence (WES) analyses and its pipeline to identify variants from exome sequence data. Our pipeline includes open source tools that include a number of tools from quality check to variant calling (see Software section).