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 |
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