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.
Haplotype caller, multisample calling on set of 9 solid and 1 ilumina sample
How does the haplotype caller handle multiple samples? Does it do a local denovo assembly for every sample and then compare those or does it do 1 local denovo assembly using the reads of all the samples?
Can I run the haplotype caller on a set of 9 solid (50bp fragment and 50 x 35 PE) together with 1 ilumina sample (100 x 100 PE) ?