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.
CNV in GATK-220.127.116.11
I'm trying to perform copy number variation analysis on my BAM files. I started with this tutorial: https://gatkforums.broadinstitute.org/gatk/discussion/9143/how-to-call-somatic-copy-number-variants-using-gatk4-cnv/p1 but I found that some scripts (like CalculateTargetCoverage) are no longer used. I was wondering if there is an updated pipeline to perform the analysis.