Table 1

Comparison of the present method with other methods

Method

Parts of the read used

Thresholds

Expected haplotype number

False positives

False negatives

Reference


CRISP

All

-4; -1,000; -1,000

20

5

0

[15]

All

-4; -1,000; -1,000

50

4

0

SPLINTER

First 12 bp

-1.301

20

2

12

[17]

First 70 bp

-6.6

20

123

0

First 12 bp

-1.301

50

2

12

First 70 bp

-6.6

50

634

0

MAQ

All

60

20

848

3

[31]

All

60

50

1,130

3

All

200

20

0

6

All

200

50

1

8

VarScan

All

1e-10

NA

190

0

[30]

Poisson

All

10

NA

0

0

Our method

Fisher exact

All

10

NA

0

0

Our method

Empirical

All

10

NA

0

0

Our method


NA, not applicable.

Li and Stoneking Genome Biology 2012 13:R34   doi:10.1186/gb-2012-13-5-r34

Open Data