If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.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.
How to interpret output of ContEst
I've recently started using ContEst and now I'd like to understand exactly what I get in the output file. What does each column mean?
-Are "contamination", "confidence_interval_95_width", "confidence_interval_95_low", "confidence_interval_95_high" fractions or percentages?
-What does "sites" represent?
I also have some questions regarding the following statistics printed to the screen:
INFO 14:38:48,617 ContEst - Population informed sites: 314
INFO 14:38:48,618 ContEst - Non homozygous variant sites: 277
INFO 14:38:48,618 ContEst - Homozygous variant sites: 37
INFO 14:38:48,619 ContEst - Passed coverage: 35
INFO 14:38:48,619 ContEst - Results: 10
-What is the coverage threshold which 35 sites have passed here? Can this threshold be set?
-What does the "Results" number refer to? I've noted that it is the same number as in the "sites" column in the output file.