Variant Calling from RNA-seq Data Using the GATK Joint Genotyping Workflow

The Genome Analysis Toolkit (GATK) developed at the Broad Institute provides state-of-the-art pipelines for germline and somatic variant discovery and genotyping. Unfortunately, the fully validated GATK pipeline for calling variant on RNAseq data is a Per-sample workflow that does not include the recent improvements seen in modern workflows, especially the possibility to perform joint genotyping analysis. Here, we describe how modern GATK commands from distinct workflows can be combined to call variants on RNAseq samples. We provide a detailed tutorial that starts with raw RNAseq reads and ends with filtered variants, of which some were shown to be associated with bovine paratuberculosis.