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.
GATK 3.5: CRAM file error with samtools-1.3
I recently created a cram file using PrintReads and tried to view the file with samtools-1.3. The header could be viewed just fine, but after the header ended the file was considered to be truncated. I received the following error:
Failed to populate reference for id 0
Unable to fetch reference #0 10001..893888
Failure to decode slice
[main_samview] truncated file.
The cram file size seems appropriate and could even be converted back to a BAM file with PrintReads successfully. I am not sure if this is a compatibility issue and if so is there a fix in the works.