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.
I'm trying to SVpreprocess some bam files but I keep getting errors stating that the bam files are not properly ordered:
RCCache: Read coordinate chr22:23242120 precedes earliest allowed read coordinate chr22:23243001 - input bam files are out of order?
This actually happens on every chromosome at different positions.
I've used Picard ResortSam and coordinate sorting with both samtools and picard for preparing the bam files, but I keep getting these errors. Does anyone have any more ideas on this?