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.
difference between Mutect 1.1.7 and MuTect2
I am trying to detect somatic Snps in a normal/tumour pair. I tried MuTect2 under Gatk (java -jar GenomeAnalysisTK.jar -T MuTect2) and varscan 2. To my surprise, there was very little overlap between the predictions ( < 1%). In a paper, varscan2 and mutect had more in common but the paper had tested the stand alone mutect (mutect 1.1.4). I tried that but it wasnt compatible with my java7 environment so I tried stand alone mutect 1.1.7 instead (java -Xmx2g -jar mutect-1.1.7.jar --analysis_type MuTect).
To my surprise, there is still a big difference between the "Pass" predictions of Mutect2 and the "Keep" predictions of mutect 1.1.7 which are also very different from varscan2... Is this normal? What do I trust?
I certainly expected more overlap...