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Table 1 The performance of HapCut versus PPHS.

From: Haplotype reconstruction using perfect phylogeny and sequence data

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

  1. 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.