The frontline support team will be slow on the forum because we are occupied with the GATK Workshop on March 21st and 22nd 2019. We will be back and more available to answer questions on the forum on March 25th 2019.
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?