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.
DepthOfCoverage -genelist: 'total coverage' and 'mean coverage' explanation
I ran DepthOfCoverage using a RefSeq interval list to use with the -genelist argument and obtained the table displaying notably the 'total coverage' and 'mean coverage' values (see here for an example).
Q1: Does the 'total coverage' make the sum of all the bases or reads mapped in each RefSeq interval provided?
Q2: How is the 'mean coverage' calculated or related to the 'total coverage'?
Does it takes the read length or gene length (or something else) into account?
Is it the value usually reported in the papers as 100X coverage for example?