Jacob R. Heldenbrand

This paper evaluates workflow management systems for genomics research and clinical use, comparing their features and suitability across different environments and use cases.

This study compares the accuracy and performance of Sentieon DNASeq and GATK for single-sample variant calling, finding they are nearly identical in accuracy with Sentieon being faster and more scalable.

The paper describes a Swift/T wrapper for the GATK variant calling workflow to improve portability and maintainability across cluster environments.

This study benchmarks GATK3.8 and GATK4 to evaluate performance improvements and cost trade-offs in genomic variant calling.