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.
symlinks to bam files
It's great that the GATK walkers can follow symlinks to bam files. But I've never understood, why GATK UG and HC can't look for the index file in the same location as the bam. Instead one has to also create symlinks to the index files in the same location as the symlinks to the bam files. This prevents one from using as input a file with bam symlinks. There are several ways to work around this, but it's just such an annoying obstacle, which I run into every 3 or 6 months, because I forget about this behaviour. Please please fix and you can come and raid my mini fridge at work full of chocolate (currently also holds LEGO). If you choose to ignore this enhancement request, then GATK is still a pretty good tool
If you have no clue what I'm talking about, then feel free to delete this ticket. It's just one of those small nuisances...