RNAseq variant calling workflow

Introduction

This small RNA variant calling pipeline provides a solution to process RNA sequencing data for RNAseq variant calling. The pipeline is built in Snakemake using GATK can be run on different platforms and high performance computing (HPC) systems.

Installation

To install this workflow, clone the repo:

git clone https://github.com/sinanugur/RNAseq-variant-calling.git
cd RNAseq-variant-calling

Quick start example

You should create a new directory called data and place your FASTQ files or their symbolic links into data/ directory. This will trigger a workflow run immediately using 15 threads:

snakemake -j 15 --use-conda

Workflow summary and DAG plot

We followed the GATK RNAseq short variant discovery pipeline.

Our Snakemake DAG plot.

Funding

The study was funded by the European Union’s Horizon 2020 research and innovation program (grant 825741).