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.
CRAM support timeline
With the recent release of improvements to sequencing my poor disks are threatened with an influx of more data than ever and I've been trying to figure out ways of reducing the amount of space each sample takes up on our fast compute disks (as well as the time it has to spend there). One of the approaches I am exploring is the use of CRAM (in lossless mode initially) in place of BAM as our primary binary reads format as it seems likely to become the preferred format of the ENA/EGA the SRA where we archive our BAMs.
A samtools version that will support CRAM will be released in a few weeks; CRAMtools hacks support into Picard but at the moment I'm stuck using BAM for steps with involve GATK. I was wondering if this was likely to change in the near future, if so whether it's likely to be weeks, months or undefined as yet wish list?