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Table 3 Comparisons between array-called and sequence variant genotypes

From: Accurate sequence variant genotyping in cattle using variation-aware genome graphs

 

Genotype concordance

Non-reference sensitivity

Non-reference discrepancy

Full

Filtered

Full

Filtered

Full

Filtered

Raw

Imp

Raw

Imp

Raw

Imp

Raw

Imp

Raw

Imp

Raw

Imp

GATK

95.99***

99.32***

96.02***

99.39***

93.81***

99.36

93.67***

99.15

6.35***

1.05***

6.3***

0.95***

Graphtyper

97.71

99.46

97.75

99.52

98.26

99.35

97.91

99.00***

3.53

0.83

3.47

0.73

SAMtools

97.68***

99.24***

97.7*

99.29***

98.21

99.35

97.53***

98.67***

3.6**

1.17***

3.56**

1.09***

  1. Genotype concordance, non-reference sensitivity and non-reference discrepancy (in percentage) were calculated between the genotypes from the Bovine SNP Bead chip and sequence–derived genotypes for 49 Original Braunvieh cattle considering either the raw or imputed (Imp) sequence variant genotypes before (Full) and after (Filtered) variants were filtered based on commonly used criteria. Asterisks denote significant differences (*P ≤ 0.05, **P ≤ 0.01, ***P ≤ 0.001) with the best value (italic) for a respective parameter
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Genetics Selection Evolution

ISSN: 1297-9686