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.
coverage confusion in mutSig. Why there are covered bases with categ=7 and effect="silent/noncoding"
Dear Mutsig Developers,
I am trying to understand the algorithm more.
I used the coverage file from the TCGA Lung Squamous paper provided from the mutSig website. However, the file really confuses me. When I do a cross tabulation, there are many bases with categ = 7 and effect = "silent" or "noncoding". This doesn't make sense to me because I thought all the 7th category (null mutation) should necessarily fall in the coding region and have a non-silent effect (which is true for the maf file). Could someone explain this a little?
Thanks a lot.