HaploRec: efficient and accurate large-scale reconstruction of haplotypes

BMC Bioinformatics

Table 2 Comparison of methods on simulated data sets with 33 kb marker spacing.

Method	Switch accuracy	No. of markers	Time per marker (sec.)
HaploRec-S	0.990	100	19.2
HaploRec-VMM	0.980	100	5.2
(HaploRec-S)	(0.969)	(30)	(6.6)
(HaploRec-VMM)	(0.970)	(30)	(2.5)
Phase	0.981	30	1585
fastPhase	0.858	20	61.3
PL-EM	0.938	30	0.9
Snphap	0.921	30	0.4
Gerbil	0.745	5	2.6

For each method, the table gives the accuracy, the number of markers to be haplotyped at a time to achieve that accuracy, and the running time per marker. As 30 marker windows are optimal for many methods, results for them are given in parenthesis also for the HaploRec variants.

ISSN: 1471-2105