NGS Variant Calling Workflow

Description

Analysis of whole-genome sequencing (WGS) data from BioProject PRJEB62494 (tongue cancer samples and cell lines) using:

• Tools: GATK, BWA, Samtools, SRA Toolkit
• Reference Genome: hg38 (chromosomes 6 & 7)

Workflow Steps

1. Download raw data using SRA Toolkit.
2. Download Refrence genome and index with BWA.
3. Quality control with FastQC/fastp.
4. Alignment with BWA-MEM.
5. Variant calling with GATK HaplotypeCaller/Mutect2.
6. Annotation using ENSEMBL VEP.

View Full Workflow Code →