David Benjamin, PhD and Samuel Lee, PhD, "The New and Improved GATK 4"

Thursday, February 1, 2018 - 12:30pm
Event Topics: 
Open Insights Seminar

David Benjamin, PhD and Samuel Lee, PhD

Computational Biologists

Broad Institute Data Science Platform


Thursday, February 1, 2017

12:30-1:30 PM


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.