Table 1 Comparison of SNV calling methods.

From: Reliable detection of subclonal single-nucleotide variants in tumour cell populations

 

SNV frequency

Errors

CPU time

 

10 −1

10 −2

10 −3

10 −4

10 −5

  

Truth

101

46

57

44

36

5,740*

 

deepSNV FDR <0.05

101

46

53

3

0

2

141 s

deepSNV FWER <0.05

99

46

49

0

0

0

141 s

VarScan17 pileup2snp

96

42

26

32

8

472

361 s†

VarScan somatic

50

29

34

1

0

33

439 s†

CRISP18

91

43

46

0

0

16

44 h

vipR19

98

43

30

0

0

1

279 s†

  1. Abbreviations: CPU central processing unit; FDR, false discovery rate; FWER, family-wise error rate; SNVs, single-nucleotide variants
  2. *Number of negatives=4 tests×1,512 positions−284 SNVs−24 masked positions (23 validated subpopulation and 1 alignment artefact).
  3. †Including 260 s for the samtools pileup command.
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