If you happen to see a question you know the answer to, please do chime in and help your fellow community members. 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.
HaplotypeCaller and Reduced Reads
I noticed that the statement "The interaction between the HaplotypeCaller and ReducedReads is still being worked out" is not in Guidebook of the lasted version (2.5.2) now. Does it mean that HaplotypeCaller now works well with Reduced BAMs and has the same accuracy as calls from un reduced BAMs, like UnifiedGenotyper? If this is true, it will certainly reduce the processing time of calling variants. Thanks in advance.