Table 1

The performance of HapCut versus PPHS.

Algorithm

Test 1

Test 2

Test 3

Test 4


HapCut - No Calls

20.85

20.63

18.67

18.03


HapCut - Errors

15.92

8.71

24.80

15.56


Beagle

2.76

1.81

2.20

1.09


PPHS

2.43

1.20

1.71

0.24


All tests were done with 5 individuals, tests 1-3 had an expected coverage of 5 while test 4 had an expected coverage of 20. Tests 1,3 had a sequencing error rate of 5% and tests 2,4 had a sequencing error rate of 1%. The read length of tests 1,2 was 400 while for test 3,4 it was 2000 bases. The cells are the percent of Switch-Mismatch errors in the data.

Efros and Halperin BMC Bioinformatics 2012 13(Suppl 6):S3   doi:10.1186/1471-2105-13-S6-S3

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