The discovery of DNA variants from Whole Exome Sequencing data remains challenging and algorithmically complex. The Moulos lab developed a protocol for consolidated variant calling which spares researchers from benchmarking different methods.
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, the algorithms that are being used for the analysis and the ever-growing data landscape. Research in the Moulos lab has led to a protocol for consolidated and unbiased WES analysis, using three variant callers (HaplotypeCaller, FreeBayes, and DeepVariant), which have different underlying models. The protocol provides detailed execution steps, as well as basic variant filtering, annotation, visualization, and consolidation aspects along with basic instructions for visualization and further downstream analysis guidelines.