Benchmarking phasing software with a whole-genome sequenced cattle pedigree

BMC Genomics

Table 3 Pairwise SNP phasing accuracy at different distances in both scenarios. Pairwise SNP phasing accuracy at distances of respectively 0.01, 0.1, 1, 2, 5, 10 and 50 Mb, obtained with AlphaPhase1.3, Beagle4.1, Beagle5.2, Eagle2.4, FImpute3.0 and ShapeIT4.1, computed for the 98 validation individuals in each scenario (scenario 1: using the 98 validation individuals; scenario 2: using the 264 sequenced individuals)

Pairwise SNP distance (Mb)	0.01		0.10		1		2		5		10		50
Scenario	1	2	1	2	1	2	1	2	1	2	1	2	1	2
AlphaPhase1.3	0.91	0.91	0.83	0.84	0.50	0.51	0.33	0.35	0.14	0.15	0.05	0.05	0.00	0.00
Beagle4.1	0.95	0.96	0.92	0.95	0.81	0.91	0.73	0.87	0.57	0.77	0.40	0.64	0.03	0.14
Beagle5.2	0.97	0.97	0.96	0.97	0.92	0.95	0.89	0.92	0.79	0.85	0.66	0.75	0.16	0.24
Eagle2.4	0.95	0.97	0.91	0.96	0.67	0.88	0.52	0.81	0.30	0.64	0.15	0.46	0.00	0.05
FImpute3.0	0.93	0.98	0.89	0.97	0.68	0.95	0.54	0.92	0.31	0.84	0.15	0.75	0.00	0.31
ShapeIT4.1	0.97	0.98	0.96	0.97	0.92	0.95	0.88	0.93	0.78	0.87	0.66	0.77	0.17	0.27

ISSN: 1471-2164