Exome Variant Detection
This pipeline is geared towards Illumina sequencing data. The BWA aligner (BWA-mem algorithm) is the most popular aligner for DNA-Seq data. After alignment, mapped reads are filtered to remove duplicates. Variant calling is performed using Freebayes, a robust variant caller that has been shown to perform well in numerous studies comparing variant calling tools. Called variants are then annotated using a transcript model and variant database to define the location of variants with regards to genes and identify known/novel variants, respectively. The view variants tasks provides a tabular representation of variants found in each sample. Suggested downstream tasks include filtering the variants based on variant quality metrics and annotation using the filter variants task, as well as functional prediction using the SnpEff and/or VEP annotation task(s). If this pipeline is used on a cohort of samples, the cohort mutation summary can be used to tabulate variants across samples. This pipeline is not optimized for Ion Torrent data or amplicon-based sequencing.