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.
FastaAlternateReferenceMaker output contig names?
Is there any way to make the output from FastaAlternateReferenceMaker not rename the contigs?
I'm running a pipeline that (theoretically) has worked with previous verions of GATK ( https://github.com/justin-lack/Drosophila-Genome-Nexus) but is now broken because FastaAlternateReferenceMaker renames contigs.
I can fix with a one-liner but wondered if there was a native GATK option?