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.
Creating a reference genome for DepthOfCoverage
I am trying to use DepthOfCoverage to analyse some sequencing I have done in Sacccaromyces cerevisiae.
I have had some problems creating the reference genome, dict and index files. First, the reference contained a non-IUPAC character which turned out to be /n (line break). I removed all instances of the character and remade the index and dict, but now the index file is incorrect. Instead of listing all the contigs, it contains only the single line
tpg|BK006935.2| 0 12274494 -1 -1
which I think refers only to the first chromosome.
I'd be very grateful for any assistance.