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

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.

SUBMITTER: Verrou KM 

PROVIDER: S-EPMC9163752 | biostudies-literature | 2022 Jun

REPOSITORIES: biostudies-literature

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

Verrou Kleio-Maria KM   Pavlopoulos Georgios A GA   Moulos Panagiotis P  

STAR protocols 20220530 2

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 conso  ...[more]

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