Wrapper around nf-core/rnavar pipeline, to analyse RNA-seq (Illumina mRNA) data from GIAB

Reads are aligned using STAR, variants called with GATK HaplotypeCaller and annotated with ENSEMBL VEP

This script requires an activated Conda environment with:

• nf-core/tools
• Singularity
• Nextflow

It can be obtained with following commands:

conda create --yes --name irmb --channel conda-forge --channel bioconda --channel defaults nf-core singularity nextflow=22.10
conda activate irmb

# Then clone present repository and move inside it:
git clone https://github.com/tetedange13/IRMB.git
cd IRMB

Simply run:

./run_pipeline.sh

After pipeline complete, result files will be under rnavar sub-directory

• Only chr22 from GRCh37 is analyzed

• Recommended "base recalibration" step is skipped

• A STAR index is built with a given read length that should match read length of processed FASTQ. Here iGenomes' index is 100 pb and GIAB data are 150 pb