Optimizing Variant Calling for Human Genome Analysis: A Comprehensive Pipeline Approach

Abstract

The identification of genetic variations in large cohorts is a critical issue to identify patient cohorts, disease risks, and to develop more effective treatments. To help this analysis, we improved a variant calling pipeline for the human genome using state-of-the-art tools, including GATK (Hard Filter/VQSR) and DeepVariant. The pipeline was tested in a computing cluster where it was possible to compare Illumina Platinum genomes using different approaches. Moreover, by using a secure data space we provide a solution to privacy and security concerns in genomics research. Overall, this variant calling pipeline has the potential to advance the field of genomics research significantly, improve healthcare outcomes, and simplify the analysis process. Therefore, it is critical to rigorously evaluate these pipelines’ performance before implementing them in clinical settings.