How to calculate read depth and coverage for whole exome sequencing?

Question

[mangfu100]

Hi all

I am struggling to find a tool for extracting the read depth information and sequence coverage. I know their information is very important before variant callings. It is necessary tasks. I found some good tools such as bedtools and used them to extract what I want. However, I failed. What I want is align information as below:

For example:

total_coverage(X) : 93.22
coverage 1X : 99.96
coverage 2X : 99.9
coverage 3x: 98.4
.....
coverage 97X : 37.39
coverage 98X : 35.54
coverage 99X : 35.79
coverage 100X : 35.27

I think these are the combination of read depth and coverage information. Although I calculate those information using bedtools, it is too laborious and I am not sure that what I am doing is right way. Could you tell me the tools or a way to extract those coverage/depth information? I already found some posts regarding this issue, but it was outdated (maybe 3~5 years ago) so it was not useful!

[Amitm]

hi,

I had the same issue. See Pierre's answer below. I would like to point to another utility in GATK: CallableLoci. This is not for depth calculation but it gives the number of bases that were 'called' at your thresholds (mapQ & depth). This info is very useful when you want to calculate the SNV/ mut. load.

Answer 1

[Pierre Lindenbaum]

see gatk depthofcoverage: https://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_gatk_tools_walkers_coverage_DepthOfCoverage.php