Assessing NGS Reproducibility: Comparative Analysis of Student-Generated VCF Files

Reproducibility is a critical consideration in bioinformatics research. Several factors can influence the consistency of results produced by a variant calling pipeline. We conducted a study in which we collected and analyzed variant call files (VCFs) generated by undergraduate computer engineering students enrolled in our Introduction to Bioinformatics course. Despite providing detailed instructions and moderation, achieving consistent results remains challenging. Factors such as hardware configurations and the choice of software platforms significantly impact the accuracy of variant calling processes.