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.
Should SplitNCigarReads still be run even though BWA was the aligner used?
We are working with 176 BAMs that were aligned using BWA and have just finished the
AddOrReplaceReadGroupsstep of the RNAseq workflow. The next step,
SplitNCigarReads, appears to assume that STAR aligner was used - is this still applicable to a BWA-aligned BAM or should we skip this step?