We’re moving the GATK website, docs and forum to a new platform. Read the full story and breakdown of key changes on this blog.
If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.We appreciate your help!
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.
Using the GATK API to annotate my VCF
I just quickly wrote a set of Tools to annotate my VCFs ( http://plindenbaum.blogspot.fr/2013/02/4-tools-i-wrote-today-to-annotate-vcf.html )
For example, one of those tools uses a BED/XML file indexed with tabix to annotate my VCF . (My code just uses the java api for tabix to get the XML at a given position)
Question: is there something in the GATK-API that would allow me to implement my code using the GATK-API: What kind of walker should I use ? What would be the benefits of using the GATK-API ? for example does using a gatk-walker will automatically make my code parallelizable ?