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bioRxiv · 10.1101/2020.05.31.126144

Implementation of Genomic Variant Calling: A Novel Approach

Kumar, A.·Bangash, A. H.
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Abstract

Genomics has emerged as one of the major sources of big data. The task of augmenting data-driven challenges into bioinformatics can be met using technologies of parallel and distributed computing. GATK4 tools for genomic variants detection are enabled for high-performance computing platforms - SPARK Map Reduce framework. GATK4+WDL+CROMWELL+SPARK+DOCKER is proposed as the way forward in achieving automation, reproducibility, reusability, customization, portability and scalability. SPARK-based tools perform equally well in genomic variants detection with that of standard implementation of GATK4 tools over a command-line interface. Implementation of workflows over cloud-based high-performance computing platforms will enhance usability and will be a way forward in community research and infrastructure development for genomic variant discovery.

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Kumar, A., Bangash, A. H.. 2020-06-01. Implementation of Genomic Variant Calling: A Novel Approach. https://doi.org/10.1101/2020.05.31.126144

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