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I also find it useful for filtering for variants with a particular concordance state (ex. FP).\r\n\r\nIt should also be possible (not implemented here) to re-compute the genotype concordance metrics using the new output.  This would be useful if you want to remove variants based on some criteria (ex. low-frequency, info/format tag/value) and re-compute the metrics.  Of course, one could always filter the original input VCF that is given to `GenotypeConcordance`.\r\n\r\n(@yfarjoun `||` @tfenne `||` @droazen) would you mind taking a 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