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

Autor:	Verrou KM; Center of New Biotechnologies & Precision Medicine, Medical School, National and Kapodistrian University of Athens, Athens, Greece., Pavlopoulos GA; Center of New Biotechnologies & Precision Medicine, Medical School, National and Kapodistrian University of Athens, Athens, Greece.; Institute for Fundamental Biomedical Research, Biomedical Sciences Research Center 'Alexander Fleming', Vari, Greece., Moulos P; Center of New Biotechnologies & Precision Medicine, Medical School, National and Kapodistrian University of Athens, Athens, Greece.; Institute for Fundamental Biomedical Research, Biomedical Sciences Research Center 'Alexander Fleming', Vari, Greece.
Jazyk:	angličtina
Zdroj:	STAR protocols [STAR Protoc] 2022 May 30; Vol. 3 (2), pp. 101418. Date of Electronic Publication: 2022 May 30 (Print Publication: 2022).
DOI:	10.1016/j.xpro.2022.101418
Abstrakt:	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. Competing Interests: The authors declare no competing interests. (© 2022 The Authors.)
Databáze:	MEDLINE
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