GATK Development
From GSA
Contents |
Programming in the GATK
Development Environment
Writing Code
- Coding standards
- Your first walker
- Managing user input
- Managing walker data presentation and control flow
- Managing and filtering reads
- Writing and working with reference metadata classes
- Collecting output
- Handling errors
- 20-Line Lifesavers: Coding simple solutions in the GATK -- Sept. 2011
Testing
- Running GATK test suites
- Writing unit tests
- Writing integration tests
- DiffObjectsWalker and SummarizedDifferences
- Running Findbugs
- Using Google Caliper for performance optimization
Documentation
Handling indels
- Seeing deletion spanning reads in LocusWalkers
- Representing Indels and other complex events and working with them with Variant Contexts
Contributing to the GATK
Tribble Development
- Tribble -- Tribble's main page has more information about the common reference meta-data library.
- Updating the Tribble library
