D3b/COV-IRT RNAseq SNV Calling Workflow (beta)

This workflow more closely follows how Broad runs in their WDL (no splitting of files nor intervals until haplotype call). Splitting (aside from haplotype calls) during bam pre-processing steps causes differences in overlap of calls and is not yet considered reliable without extensive benchmarking. It follows the COV-IRT pipeline except for gVCF generation. Preparation for joint calls is not part of this workflow and is more of a single sample call style.