This section contains articles related to developing for the GATK. Topics covered include how to write new walkers and Queue scripts, as well as some deeper GATK engine information that is relevant for developers.
The documentation articles in this section cover:
Please note that while many of the articles contain command lines and argument values, these are given as examples only and may not be the most appropriate for your dataset. It is your responsibility to ascertain that the parameters you use for analysis make sense considering your experimental design and materials.
In addition, certain examples, argument names, usages and values may become obsolete over time. We try to update the documentation regularly but some articles may fall through the net. This occasionally leads to apparent contradictions between articles in this section and the Technical Documentation that is available for each tool. When in doubt, keep in mind that the Technical Documentation is updated more frequently and always trumps other documentation sources.
This section lists (and answers!) frequently asked questions.
These documentation articles cover specific points of clarification about the following:
Information about forum features and events impacting support will be announced here.
Only forum administrators and moderators are able to post new discussions. Please feel free to comment on existing discussions.
This is the place to post any questions, problems or bug reports for the GATK development team to look at.
We try to respond within a reasonably short amount of time, but keep in mind that we are not support agents -- we are programmers and scientists, with code to write and data to analyze. In the same spirit, because our resources are limited and our time precious, we ask that you please consult all available sources of information in the GATK Guide and previous posts in this forum before posting your question here, and above all, refrain from posting problems that are clearly identified as USER ERRORS in the GATK's output. Thank you!
We also welcome discussions and responses from everyone in the user community. If you know something, say something!