The Genome STRiP team is based at the Broad Institute and at the McCarroll Lab in the Harvard Medical School Department of Genetics.
Bob Handsaker, Methods and Software Development
Seva Kashin, Methods and Software Development
Alec Wysoker, Methods and Software Development
Steve McCarroll, Principal Investigator
We would also like to thank the following people:
Josh Korn, Jim Nemesh and Milan Kantesaria for significant contributions to the development of the methods embodied in Genome STRiP.
Vanessa Van Doren, ddPCR goddess.
Giulio Genovese, Amnon Koren, Linda Boettger, Christina Usher, Aswin Sekar and Chris Whelan have been close collaborators from within the Broad/HMS community on a number of projects involving applications of Genome STRiP.
Jen Berman, Dimitri Skvortsov, Michael Thornton, Niels Klitgord, Bin Zhang and Svilen Tzonev, our collaborators from the Digital Biology Center of Bio-Rad Laboratories, have helped us understand how to use and optimize droplet digital PCR (ddPCR) technology for assessment of copy number variation.
Our work has benefitted greatly from numerous conversations with Nick Patterson, Brian Browning, Heng Li, Matt Hurles, Mark de Pristo and all of the members of the 1000 Genomes Project Structural Variation and Analysis Groups.
Genome STRiP utilizes the following major software tools and libraries
The Genome Analysis Toolkit (GATK)
Picard / SAM JDK
The R Project for Statistical Computing