Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
Writing custom tools: htsjdk vs picard vs GATK
Hi fellow htsjdk/picard/gatk developers!
I've been thinking about this for quite some time now, so I thought I should write up a quick post about it here.
I've been writing custom tools for our group using both picard and GATK for some time now. It's been working nicely, but I have been missing a set of basic tutorials and examples, for users to quickly get started writing walkers. My most commonly used reference has been the 20-line life savers (http://www.slideshare.net/danbolser/20line-lifesavers-coding-simple-solutions-in-the-gatk) which is getting a bit dated.
What I would like to see is something like for following:
- What's in htsjsk? What's not in htsjdk? (from a dev's perspective - in terms of frameworks)
- What's in picard? What's not in picard? (from a dev's perspective - in terms of frameworks)
- What's in gatk? What's not in gatk? (from a dev's perspective - in terms of frameworks)
- When to use htsjdk, picard any GATK. What are the strengths and weaknesses of the three. (possibly more that I've missed)
- Your first htsjdk walker
- Your first picard walker
- Your first gatk walker
- Traversing a BAM in htsjdk vs gatk - what are the differences
There might be more stuff that could go in here as well. The driving force behind this is that I'm myself a bit confused by the overlap of these three packages/frameworks. I do understand that picard uses htsjdk, and that GATK uses both as dependencies, but it's not super clear what extra functionality (for a developer) is added from htsjdk -> picard -> gatk.
Could we assemble a small group of interested developers to contribute to this? We could set up a git repo with the examples and tutorials for easy collaboration and sharing online.
Anyone interested? I'll could myself as the first member