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.
setup local picard against local htsjdk
Since I am not having success using picard on my cram files, I decided to setup the picard source code along with the htsjdk source code locally, where I put htsjdk (folder with the same name) under the picard folder.
Here is the problem. I am trying to link my local htsjdk with my local picard code, but there is no documentation regarding this.
There is an old thread on this https://gatkforums.broadinstitute.org/gatk/discussion/6826/picard-build-cant-find-htsjdk, but somehow they didn't explicitly give an answer to the very question they try to answer. They provided all other links except the one that answer the question!
It is possible that I have missed the place where the answer is. Please direct me to the right direction. Thank you very much!