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VQSR Resources for Indels
I noticed that on the page for setting the right arguments for VQSR you mentioned that Mills and dbSNP should be used as resources for INDEL variant recalibration. However, at the bottom of the page, it is said that the apply recalibration step for INDELs should use Mills and 1000G. Since these two tools are used together, I would like to know which combination of resource files to pass on to them: Mills/dbSNP or Mills/1000G.