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.


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