Forum: Ryan Poplin of GATK uses this
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gravatar for Istvan Albert
3.5 years ago by
Istvan Albert ♦♦ 76k
University Park, USA
Istvan Albert ♦♦ 76k wrote:

Ryan Poplin holds a Bachelor of Science in Computer Science and Mathematics from Rose-Hulman Institute of Technology (2004) and a Master of Science in Neural Computation from Carnegie Mellon University (2009). He joined the Broad Institute in October of 2009 and has developed several methods such as Base Quality Score Recalibration and Variant Quality Score Recalibration. Today he serves as the team of leader for the methods development for the Genome Analysis Toolkit: GATK

Over the years GATK has proven itself to be the "de-facto standard" when it comes to variant discovery and genotyping. Any and all new tools and methodologies are measured against it -  make not mistake, in science it is hard to be the "king" - everyone is out to get you. But they are busy kings - continuously improving GATK, adding new functionality,  focusing on usability and accessibility. Their forums are unique in both the quantity and quality of answers and support that they provide to their user community. That too should be an example to follow. 

Special thanks go to Géraldine Van der Auwera for providing the following background information on GATK:

"GATK has evolved enormously over the past few years. It was originally conceived as an in-house development framework for savvy analysts within the Broad to easily write new analysis tools. And it was indeed used in that capacity for the development of tools like GenomeSTRiP (by Bob Handsaker) and MuTect (by Kris Cibulskis). But at the same time, the core development team was increasingly being tasked with developing tools to accomplish specific analytical goals in the context of projects like the 1000 Genomes, which brought about the core variant discovery tools that form the backbone of the well-known Best Practices. And that's essentially how the GATK went from being a development framework to a toolkit that scientists worldwide use as an out-of-the-box solution.

Nowadays the team (~12 people, mostly computational biologists and software engineers) develops tools and methods to fulfill the needs of the Broad sequencing pipeline, plus specific analysis projects as the need arises. The team's two major areas of focus are on overcoming scaling issues and on developing novel methods to push the boundaries of analysis in areas that pose particular challenges (e.g. RNAseq, CNVs and SVs, somati/cancer analysis and so on). This involves a lot of really interesting collaborations with experts in those fields. Like the GATK itself, the development team has gone through a lot of transformations over the past few years, to accommodate evolving needs and priorities --and there is more change on the way!

But that's a story for another time. Point is, Ryan Poplin has been with the team for most of its history, and is now leading the methods development unit. As such, he charts the course for GATK methods development and plays a key role in determining both the objectives and implementation of new GATK capabilities."


Ryan Poplin of GATK

What hardware do you use? 
Development is done on a MacBook Pro laptop. I connect to an Apple retina display to maximize my IGV knowledge potential. For computation I use the Broad Institute's linux cluster.

What is your text editor?
IntelliJ for pretty much everything.

What software do you use for your work?
GATK and IGV for everything genomics related. Other programs that are almost always open are HipChat, Safari, and the basic mac terminal.

What do you use to create plots and charts?
ggplot2 -- so awesome.

What do you consider the best language to do bioinformatics with?
They are all about the same to me. Whichever language allows you to try out your new ideas the quickest is probably best.

What bioinformatics tools/software do not get enough recognition?
I've been surprised by the number of people who are using bwa but not yet bwa mem.


See all post in this series https://www.biostars.org/t/uses-this/

To be notified of a new post in the series follow the first post: Jim Robinson of the Integrative Genomics Viewer (IGV) uses this

uses-this forum • 3.1k views
ADD COMMENTlink modified 3.4 years ago by Danielk550 • written 3.5 years ago by Istvan Albert ♦♦ 76k
0
gravatar for Danielk
3.4 years ago by
Danielk550
Karolinska Institutet, Stockholm, Sweden
Danielk550 wrote:

I gotta say, I really appreciate the "uses this" series. Good stuff. 

ADD COMMENTlink written 3.4 years ago by Danielk550
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