Isaac, the Illumina variant calling workflow

Abstract

As the pace of implementing personalized medicine concepts increases, high-throughput variant calling on hundreds of individual genomes per day is a reality that will likely be faced by sequencing facilities across the country in the near future. While the scientific best practices for human variant calling workflows have been well defined, they also pose serious computational challenges at this high scale. Therefore, efforts in both academia and the private sector have focused on developing alternative workflows that may substantially reduce the computational cost per individual genome. Isaac is an \"ultra-fast\" variant calling workflow, designed by Illumina, Inc, and is claimed to be six times faster than BWA-GATK, with comparable sensitivity and specificity. This report is an independent review of Isaac, mainly focused on the accuracy of variant calls. We note that Isaac is indeed quite fast, and provide some benchmarks on a few hardware architectures. The overall conclusion from our analysis is that the Isaac workflow has undergone substantial improvement from version 01.14.11.27 to Isaac_2.0. The call accuracy is especially high on NA12878, however exomes tend to have a high fraction of false positive calls. We did not manage to reproduce the 99% sensitivity and specificity reported in the Illumina whitepaper, however that might be improved with further tweaking of the options. This report includes the information about some of the command-line parameters and documentation.