Protocol for unbiased, consolidated variant calling from whole exome sequencing data

Kleio-Maria Verrou; Georgios A Pavlopoulos; Panagiotis Moulos

doi:10.1016/j.xpro.2022.101418

Protocol for unbiased, consolidated variant calling from whole exome sequencing data

STAR Protoc. 2022 May 30;3(2):101418. doi: 10.1016/j.xpro.2022.101418. eCollection 2022 Jun 17.

Authors

Kleio-Maria Verrou¹, Georgios A Pavlopoulos^{1

2}, Panagiotis Moulos^{1

2}

Affiliations

¹ Center of New Biotechnologies & Precision Medicine, Medical School, National and Kapodistrian University of Athens, Athens, Greece.
² Institute for Fundamental Biomedical Research, Biomedical Sciences Research Center 'Alexander Fleming', Vari, Greece.

Abstract

Whole Exome Sequencing (WES) is used for querying DNA variants using the protein coding parts of genomes (exomes). However, WES analysis can be challenging because of the complexity of the data. Here, we describe a consolidated protocol for unbiased WES analysis. The protocol uses three variant callers (HaplotypeCaller, FreeBayes, and DeepVariant), which have different underlying models. We provide detailed execution steps, as well as basic variant filtering, annotation, visualization, and consolidation aspects.

Keywords: Bioinformatics; Genetics; Genomics.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Exome Sequencing
Exome* / genetics
High-Throughput Nucleotide Sequencing* / methods

Associated data

figshare/10.6084/m9.figshare.19115102