Introduction

UCL-BLIC/rnaseq_variant_calling is a bioinformatics analysis pipeline used for calling variants on RNA sequencing data

The workflow processes raw data from FastQ inputs (FastQC, Trim Galore!), aligns the reads with STAR and does variant calling with GATK following the best practices for RNAseq data

The pipeline is built using Nextflow, a bioinformatics workflow tool to run tasks across multiple compute infrastructures in a very portable manner.

Documentation

The UCL-BLIC/rnaseq_variant_calling pipeline comes with documentation about the pipeline, found in the docs/ directory:

1. Installation
2. Running the pipeline
3. Output and how to interpret the results
4. Troubleshooting