RNAseq Variant Calling with Snakemake (Mutect2 and vardict)

This Snakemake pipeline performs variant calling on RNA-seq data using STAR for alignment and GATK for variant calling.

Steps

• Alignment: bwa-men2
• Preprocess BAM (GTAK best practices: https://gatk.broadinstitute.org/hc/en-us)
• Variant Calling Step1: GATK Mutect2 (https://gatk.broadinstitute.org/hc/en-us/articles/360037593851-Mutect2)
• Variant filtering
• Variant Calling Step2: VarDict (https://github.com/AstraZeneca-NGS/VarDict)
• (Optional) Annotation: VEP or snpEff

##Dependencies

• bwa-men2
• gatk4-4.6.1.0-0
• samtools
• VEP

Usage

conda install -c conda-forge mamba
mamba create -n snakemake -c bioconda -c conda-forge snakemake
snakemake -s Scripts/Snakefile --configfile Scripts/gatk_rnavar_config.yaml --jobs 10 --cores 80 --use-conda --conda-frontend conda --keep-going -n