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.
maxReadsForRealignment value and depthofcoverage results don't jibe; indelrealigner
indelrealigner rejects a region because there are too many reads. --maxReadsForRealignment was set to 100000 for this run. when i run the depthofcoverage tool, it show that the max coverage in the region that was rejected is ~95000. many positions are far less, like around 1000. i don't understand why this region would be rejected since no position has a depth of coverage over the max i set with --maxReadsForRealignment.