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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.
MarkIlluminaAdapters missing from GATK pipelines
The best practices GATK exome and genome pipelines seem to not perform adapter clipping/marking with MarkIlluminaAdapters as described here: https://software.broadinstitute.org/gatk/documentation/article?id=6483
This would likely lead to significant issues in subsequent alignments and false positive calls.
Why is MarkIlluminaAdapters not part of the standard GATK pipelines even though the GATK website says it should be?