RNA-VC

Variant calling pipeline for RNA-Seq data

Introduction

The script is based on the GATK best practices workflow for RNA-Seq data. https://gatk.broadinstitute.org/hc/en-us/articles/360035531192-RNAseq-short-variant-discovery-SNPs-Indels- Script developed by Aditya Singh https://github.com/aditya-88 [email protected]

The script takes in the following arguments:

1. Path to the reference genome
2. Path to the input BAM file aligned using STAR two-pass mode
3. Path to the output directory
4. Known sites for GATK BaseRecalibrator

The script performs the following steps:

1. Mark duplicates
2. Split'N'Trim and reassign mapping qualities
3. Base quality score recalibration
4. Variant calling
5. Variant filtering

The script requires the following tools to be installed:

1. GATK
2. Picard tools (for MarkDuplicates, is part of GATK)
3. STAR (for alignment, not required for this script)

Usage

bash rnavc.sh <reference genome> <input BAM file> <output directory> <threads> <memory in GB> <BED file> <GATK 4.x executable>

System Requirements

Unix/ Linux system with BASH/ ZSH
SAMTools
GATK 4.x