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Table 7 Contingency tables of genotype calling with five methods (columns) versus actual genotypes (rows)

From: A hidden Markov approach for ascertaining cSNP genotypes from RNA sequence data in the presence of allelic imbalance by exploiting linkage disequilibrium

Actual

VarScan Genotype

HMM-ASE

HMM-NASE

genotype

He

Ho

NC

He

Ho

NC

He

Ho

NC

      

(Reads =0)

  

(Reads =0)

He

449

78

64

571

0

20

570

1

20

Ho

0

886

83

9

914

46

2

921

46

Actual

SAMTOOLS + BCFTOOLS

BEAGLE

 

genotype

He

Ho

NC

He

Ho

NC

   

He

576

9

6

583

8

0

   

Ho

4

957

8

6

963

0

   
  1. Values in bold represent counts of correct calls. The other values are incorrect calls or Non-called (NC).