Table 3.

Ranking of variant-level filters for ClinVar-indexed biallelic sites, and genome-wide biallelic and triallelic sites.

Rank	Filter	Negative Predictive Value			Specificity
		Discordances among Discarded Genotypes (%)			% of Discordant Genotypes Removed
		ClinVar Biallelic	All Biallelic	All Triallelic	ClinVar Biallelic	All Biallelic	All Triallelic
1	Missingness	87.65	1.98	42.55	18.39	0.03	34.92
2	MQ	16.19	8.85	42.91	48.70	55.38	79.98
3	DP	13.97	20.72	45.97	27.46	19.21	53.34
4	VQSLOD*	12.16	6.77	41.15	55.96	68.65	99.03
5	InbreedingCoeff	2.25	2.31	29.62	4.40	3.65	37.76

The filters are ranked in order from greatest to lowest preference for filtering out discordant genotypes. Negative predictive value refers to a filter’s ability to remove discordant genotypes (true negatives) and minimize the number of concordant genotypes removed (false negatives). Specificity refers to a filter’s ability to identify and remove discordant genotypes (true negatives) and minimize the number of discordant genotypes retained (false positives). Matching was performed using ClinVar version 2019-01-02.

*Filter applied to biallelic and triallelic sites involving only SNVs.