Table 3. Bias and MSE of mapgd, VCFtools, KING, and PLINK in estimating coancestry, fraternity, and inbreeding for outbred and inbred siblings.

Coancestry (Θ)		Out. $\left(\mathrm{\Theta }=1/4\right)$		In. $\left(\mathrm{\Theta }=1/2\right)$
Program	Cov.	Bias (×103)	MSE (×104)	Bias (×103)	MSE (×104)
mapgd	3×	−10	2.2	−11.6	2.5
VCFtools	3×	−68	50	−150	230
KING	3×	−120	170	−450	2000
mapgd	10×	−6.9	0.73	−8.2	1.5
VCFtools	10×	−12.0	1.8	−16	3.3
KING	10×	−21	4.7	−520	2700
mapgd	30×	−6.4	0.69	−7.2	1.0
VCFtools	30×	−5.7	0.70	−4.5	1.0
KING	30×	−3.1	0.29	−500	2500
Fraternity $\left({\mathrm{\Delta }}_{\ddot{X}\ddot{Y}}\right)$		Out. $\left({\mathrm{\Delta }}_{\ddot{X}\ddot{Y}}=1/4\right)$		In. $\left({\mathrm{\Delta }}_{\ddot{X}\ddot{Y}}=3/8\right)$
Program	Cov.	Bias (×103)	MSE (×104)	Bias (×103)	MSE (×104)
mapgd	3×	−7.2	22	−0.3	23
PLINK	3×	−20	7.1	72	52
KING	3×	370	1400	230	520
mapgd	10×	−1.7	4.3	−1.4	5.8
PLINK	10×	11	2.3	110	120
KING	10×	58	36	400	1700
mapgd	30×	1.2	4.3	8.6	6.1
PLINK	30×	1.7	1.6	120	150
KING	30×	−3.5	1.7	360	1300
Inbreeding $\left(f_X\right)$		Out. $\left(f_X=0\right)$		In. $\left(f_X=1/2\right)$
Program	Cov.	Bias (×103)	MSE (×104)	Bias (×103)	MSE (×104)
mapgd	$3\times$	−14	7.1	−33	18
VCFtools	$3\times$	99	100	−100	110
PLINK	$3\times$	72	54	−150	220
mapgd	$10\times$	−8.5	1.6	−7.0	1.3
VCFtools	$10\times$	15	3.5	−11	9.5
PLINK	$10\times$	12	2.4	−7.4	1.2
mapgd	$30\times$	−9.0	1.9	−7.6	1.6
VCFtools	$30\times$	−0.1	1.9	−3.8	1.3
PLINK	$30\times$	−2.2	1.4	−2.4	0.9

The values of all seven IBD coefficients are listed in Table S5 in File S1. Results are from 100 simulations on a 400-kbp, 400-cM genome containing $\sim 10,000$ SNPs. See Section S7 in File S1 for SNP filtering parameters. Out., outbred; in., inbred; cov. coverage. See figure S7 for diagram of outbred and inbred siblings.