Notice:
If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We appreciate your help!

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 summary reports too many bases

RaphaelKRaphaelK BaltimoreMember

I'm a bit confused about some of the output of GATK's DepthOfCoverage script.
In the *.GATK.covdepth.sample_summary, what does the "total" column signify?
Is it the total number of base pairs in the data? Because my raw read data has ~37.2 billion bp. However, GATK reports over 92 billion bp.
Does the 'total' mean something else, or will I have to rerun the DepthofCoverage script?

Thanks in advance!

Answers

Sign In or Register to comment.