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.
CalculateContamination output table
The CalculateContamination description says:
Calculates the fraction of reads coming from cross-sample contamination, given results from GetPileupSummaries ... this tool estimates contamination based on the signal from ref reads at hom alt sites.
It produces a resulting contamination table that looks something like:
level contamination error whole_bam 0.001012896128155539 1.8192151501912648E-4
I wasn't able to find an explanation of what the output actually is. Of course, I assume that "contamination" and "error" should be as close to 0 as possible, but what exactly are they? Is it contamination from potential other individuals based on population allele frequencies? What happens when there is a matched normal? Do they both need to be contaminated? What about contamination of the normal by the tumor? Those seem to be very different problems, but could both be labeled as contamination.