A Snakemake workflow for the call of Single Nucleotide Polymorphisms (SNPs) from RNA-seq data. The workflow starts from aligned .bam files and outputs variants called by FreeBayes (or GATK's HaplotypeCaller) and annotated by VEP.
The usage of this workflow is described in the Snakemake Workflow Catalog.
If you use this workflow in a paper, don't forget to give credits to the authors by citing the URL of this (original) sitory and its DOI (see above).