I was looking into the VQSR process, and could not get the role of the 'known resource'.
The fifth content of the GATK VQSR document, which explains about the usages of truth/training/known resources, explains that
known resources are used "to stratify output metrics such as Ti/Tv ratio by whether variants are present in dbsnp or not (known=true)"
I don't get how it 'stratifies' output metrics such as Ti/Tv (wonder if there's other metrics than Ti/Tv). dbsnp may have been assigned as 'known'
in this situation.
Can anyone explain this to me? Thanks in advance.