Table 1.

Analysis of FranceGenRef data. $\widehat{\phi }$ is the estimate of the two siblings’ unobserved kinship coefficient $\phi$

		WGS data at 30–40×		Down-sampled WGS data at ~ 2.5×
		Gaston Full GRM	NGS- RelateV2	LowKi (Unadjusted)*	LowKi	BEAGLE  +  LowKi	BEAGLE +  SEEKIN	NGS- RelateV2‡
Sibling Pair 1	$\widehat{\phi }$	0.258	0.268	0.122	0.278	0.265	0.268	0.256
	$\widehat{\psi }$	0.294	0.379	0.059	0.185	0.255	†	0.459
Sibling Pair 2	$\widehat{\phi }$	0.216	0.228	0.100	0.223	0.225	0.226	0.216
	$\widehat{\psi }$	0.196	0.270	0.035	0.115	0.166	†	0.367
M (number of variants)				1,009,181	1,009,181	949,075	949,075	1,009,181
Time				4 min	4 min	15 h**	15 h **	6 h

$\widehat{\psi }$ is the estimate of the two siblings’ unobserved fraternity coefficient $\psi$. (*) Unadjusted values from LowKi, similar to in Additional file 1: Fig. S2. (**) The time required for these estimators is almost entirely due to BEAGLE, both LowKi and SEEKIN require only a few minutes. (†) SEEKIN does not provide estimates of $\psi$. (‡) NGSRelateV2 results on down-sampled data should be compared to results from the same software but applied to the original data that had not been down-sampled