Table 1

Definition and size of the classes
Accuracy % Trait Time
PA (ua) Imp. (ua) PHA % Assoc. Sec Remarks
Unrelated individuals (no parent information)
fastPHASE [6] 60.07(0.00) 59.77(0.00) NA No 78
58.01(0.00) 56.55(0.00) 158
FMPH [12] - - NA No - Up to 30-100 markers
MACH [9] 52.89 (0.00) 52:16(0:00) NA Yes 567
52.49 (0.00) 50.91 (0.00) 1144
Unrelated trios
BEAGLE [5] 99.90 (0.00) 98.61 (0.00) NA Yes 5
99.90 (0.00) 98.28 (0.00) 10
HAPI-UR [8] 99.69 (0.00) 94.75 (0.00) NA No 3
99.67 (0.00) 94.88 (0.00) 7
Related trios
HAPI [7] 90.75 (9.17) 0.00 (100.0) 83.88 No 0.1 < 15 progeny/parent
90:63(9:29) 0:00(100:0) 83.87 0.2
Merlin [13] 70:59(29:38) 69:60(29:47) 69.74 Yes 299 < 15 progeny/parent
64:80(35:18) 63:72(35:09) 63.81 604
SHAPEIT2 [11] 87:20(0:00) 57:61(0:00) NA No 70 < 50 progeny/parent
90:46(0:00) 64:05(0:00) 148
iXora 95:89(4:05) 92:11(7:75)) 95.55 Yes 0.3
95:73(4:21) 91:43(8:40) 95.43 0.8

The first row for each method corresponds to 300 markers while the second to 600 markers. The results are averaged over multiple data sets of 200 individuals. Parental haplotype assignment (PHA) was found to be critical in the task of trait association in [15] and is shown here in bold font. Section Methods describes accuracy and PHA computation in detail. Trait assoc. denotes whether the software allows testing for phenotype association. Time was obtained on a system with 3.0 GHz quad-core processor and 4 GB memory. Abbreviations: PA= Parent assignment; Imp. = Imputation; PHA = Parent haplotype assignment; ua = unassigned; β€œNA” = computation is outside the scope of the software; β€œ-” = unable to compute on our data sets

Utro et al.

Utro et al. BMC Genetics 2013 14:48   doi:10.1186/1471-2156-14-48

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