Protocol for unbiased, consolidated variant calling from whole exome sequencing data
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Updated: Sep 20, 2025

Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease
Published on: April 4, 2018
Kleio-Maria Verrou1, Georgios A Pavlopoulos1,2, Panagiotis Moulos1,2
1Center of New Biotechnologies & Precision Medicine, Medical School, National and Kapodistrian University of Athens, Athens, 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.
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