David Benjamin, PhD and Samuel Lee, PhD
Broad Institute Data Science Platform
Thursday, February 1, 2017
The New and Improved GATK 4
GATK 4 is an expanded, improved, scalable, and fully open-source version of the popular genomics software. In addition to the germline variant discovery tool HaplotypeCaller, it now contains tools for copy-number, structural, and somatic variants. A rewritten engine makes developing new GATK tools easier than ever. Furthermore, the WDL workflow language enables GATK tools to be combined in robust and maintainable pipelines that run equally well on a laptop or on the cloud. After a brief survey of GATK 4, we will discuss its new pipelines for germline and somatic copy-number variants and its updated version of Mutect2 for somatic SNVs and indels, highlighting their algorithms and upcoming developments.