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Table 3 Accuracy of imputation from 50 K to sequence, with either no clustering (ALL) or PLINK haplotype clustering (PLINKH) used to determine reference population for imputation from 777 K to sequence, and different reference populations (ALL or PLINKH) having been used for imputation from 50 K to sequence

From: Novel methods for genotype imputation to whole-genome sequence and a simple linear model to predict imputation accuracy

Scenario

Overall R2

Time/Animal

Concordance

Concordance MAF < 0.05

50 K

777 K

ALL

ALL

0.819

0:03:47

0.935

0.974

PLINKH

ALL

0.810

0:03:44

0.931

0.973

ALL

PLINKH

0.817

0:02:32

0.935

0.973

PLINKH

PLINKH

0.810

0:02:28

0.932

0.973