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.
Is there a way to remove the "|" from the SQ line in a .bam file?
We have several, unique H. pylori genomes. We have aligned each of them to a reference genome, which had "|"in the fasta (or .fa) file name. Now, when running through GATK, we cannot create our final .vcf file. Do we have to remove the "|" from the .fa file and rerun everything from the beginning, or is there another approach?