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.
[GATK 4 beta] FilterByOrientationBias for matched normals
In the manual / help-page of CollectSequencingArtifactMetrics, it is said that CollectSequencingArtifactMetrics tool should be run for both the normal sample and the tumor sample, if the matched normal is available. Could you elaborate a bit how to do this, since it appears that the --preAdapterDetailFile parameter in CollectSequencingArtifactMetrics and the --input parameter in CollectSequencingArtifactMetrics cannot be defined more than once. Should I, for example, apply the CollectSequencingArtifactMetrics tool twice for the VCF files and if, yes, does the order of T and N matter.