Table 2.

False-Positive Rates for BEAGLE, GERMLINE, and PLINK for Illumina 550K European Data

Sizeb	BEAGLE			GERMLINE			PLINK (Default)			PLINK (Relaxed)a
	No. of Segments	No. of IBD SNPsc	FP Rated	No. of Segments	No. of IBD SNPsc	FP Rated	No. of Segments	No. of IBD SNPsc	FP Rated	No. of Segments	No. of IBD SNPsc	FP Rated
≥ 0.5 cM	9	1009	1.9 × 10−6	2202	581010	1.1 × 10−3	19	2118	2.2 × 10−5	100	7173	7.6 × 10−5
≥ 1 cM	1	170	3.3× 10−7	1202	365730	7.0 × 10−4	19	2118	2.2 × 10−5	97	7079	7.5 × 10−5
≥ 2 cM	0	0	0	118	43786	8.4 × 10−5	19	2118	2.2 × 10−5	76	6077	6.4 × 10−5
≥ 3 cM	0	0	0	14	3839	7.4 × 10−6	18	2016	2.1 × 10−5	41	3754	4.0 × 10−5
≥ 4 cM	0	0	0	8	1398	2.7 × 10−6	11	1273	1.4 × 10−5	20	1874	2.0 × 10−5
≥ 5 cM	0	0	0	8	1398	2.7 × 10−6	4	439	4.7 × 10−6	9	794	8.4 × 10−6

Detected IBD on chromosome 1 in 13,275 pairs constructed so as to have no IBD.

^aSee Material and Methods for parameters used in the relaxed PLINK run.

^bReported size of detected segments.

^cSum of numbers of SNPs covered by detected segments within this size category.

^dFalse-positive rate is (no. of IBD SNPs)/(nSNPs × npairs), where “nSNPs” is 39,146 for BEAGLE and GERMLINE and 7103 for PLINK (SNPs on chromosome 1) and where “npairs” is 13,275 (number of pairs tested).