Analysis of genomic variants of a patient with advanced squamous cell lung cancer (Part I)

Overview

In this case, we will process multiple FASTQ files from Whole Exome Sequencing (WES) of tumour and normal samples to generate Variant Call Format (VCF) files.

The starting files for this training were not provided due to their large size, initial state of working directory should look something like this:

.
├── env
│   └── variant_analysis_exercise.yml
├── genome
│   └── hg38_chr12.fa
├── intervals
│   └── S07604514_Padded_v6_chr12.bed
├── raw_data
│   ├── normal_1.fq.gz
│   ├── normal_2.fq.gz
│   ├── tumor_1.fq.gz
│   └── tumor_2.fq.gz
├── README.md
└── scripts
    ├── cleanup.sh
    └── pipeline.sh

Conda environment setup

The specifications of the conda environment with the necessary programs for this exercise are in env/variant_analysis_exercise.yml. To install it, use the following command:

conda env create -f env/variant_analysis_exercise.yml

Usage

To run the pipeline, navigate to the main directory and execute pipeline.sh with bash:

bash scripts/pipeline.sh

To rerun the pipeline with different samples, execute cleanup.sh to clear the working directory and manually organize the new files into their respective folders.

bash scripts/cleanup.sh