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.
understanding dcov option
Here is an excerpt of the docs of -dcov option:
"For read-based traversals (ReadWalkers like BaseRecalibrator), it controls the maximum number of reads sharing the same alignment start position."
Here are my questions:
1. which are ReadWalkers? for example, is IndelRealigner a read walker?
2. For a read walker, if read length is 100 bp, does "-dcov 1" mean the max depth at any locus is 100?