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I've been going through the VQSR documentation/guide and haven't been able to pin down an answer to how it behaves on multi-sample VCF (generated by multi-sample calling with UG). Should VQSR be run on this? Or on each sample separately, given that coverage and other statistics used to determine the variant confidence score aren't the same for each sample and so can lead to conflicting determinations on different samples.
What is the best way to go about this?