HaploShare: identification of extended haplotypes shared by cases and evaluation against controls

Table 1 Comparison of adjusted power on detecting pair-wise haplotype-sharing IBD between HaploShare, BEAGLE, GERMLINE, PLINK, DASH, and IBD-Groupon

Age of simulated regions (generations)	Length (cM)		HaploShare (multiple) ^b		HaploShare (pair-wise) ^c		BEAGLE IBD	BEAGLE fastIBD	PLINK	GERMLINE	DASH plus GERMLINE	BEAGLE plus IBD-Groupon
Age of simulated regions (generations)	Length (cM)	Threshold ^a	1 cM	0.5 cM	1 cM	0.5 cM	N/A	N/A	0.5 Mb	0.5 cM	0.5 cM	N/A
50	1.14		45.1	47.8	30.2	38.7	36.6	30.8	0.0	41.9	36.4	29.2
40	1.28		51.9	54.6	35.9	46.9	41.4	40.8	0.0	44.7	40.3	39.3
30	1.53		94.8	95.1	66.6	81.4	49.2	48.8	19.1	49.2	47.7	49.2
20	2.35		97.7	97.8	80.0	90.1	73.2	73.9	39.2	61.1	62.3	73.7
10	4.18		100.0	100.0	94.6	96.9	97.1	96.2	65.6	70.1	72.6	96.5

All results shown here are detections of pair-wise sharing reaching threshold based on respective thresholds in respective programs, no comparison to controls was involved.
^aFor HaploShare, GERMLINE, DASH, and PLINK, it is the minimum genetic distance (or physical distance) of the haplotypes shared pair-wise to be selected for further analysis; for BEAGLE, it is the prior IBD probability; for BEAGLE fastIBD, it is the fastIBD score, and for IBD-Groupon, it is also the fastIBD score.
^bHaplotypes shared pair-wise surpassing a certain genetic distance (0.5 or 1 cM) are further analyzed for sharing by multiple individuals, which by itself increases power of detecting more individuals sharing an extended haplotype (Step 4, Figure 1).
^cAnalysis stops at only detecting haplotypes shared pair-wise without merging pair-wise sharing into sharing by multiple individuals (stops at Step 3, Figure 1).

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