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Table 5 Overlap ratio of original data and HapMap data with Park and Conrad's data

From: Comparative analysis of copy number variation detection methods and database construction

Programs Average of overlap ratio of HapMap with Conrad's data[28]and Park's data[29] Average of overlap ratio of original data with Conrad's data[28]and Park's data[29] Average of overlap ratio of original data of commonly detected regions at least two programs, with Conrad's data[28]and Park's data[29] Average of overlap ratio of original data of commonly detected regions in more than two individuals, with Conrad's data[28]and Park's data[29] Average of overlap ratio of original data of commonly detected regions in more than nine individuals with Conrad's data[28]and Park's data[29]
PennCNV [8986/5619] 52.2/53.2%*$
44.6/50.8%$$
35.8/39.7%
32.1/39.0%
42.5/45.2%
42.7/48.2%
57.8/58.6%
58.6/63.9%
61.8/62.3%
62.9/68.0%
Birdseye (part of Birdsuite)
[6959/5063]
68.7/69.6%
62.9/65.6%
71.0/71.6%
81./83.2%
62.1/63.1%
71.4/74.6%
75.6/75.8%
86.7/88.5%
79.4/79.5%
91.6/92.9%
Birdsuite
[31852/25794]
66.3/66.6%
53.4/56.5%
65.0/65.3%
63.8/66.8%
65.2/65.9%
73.9/77.1%
67.9/67.9%
67.1/70.1%
70.6/70.6%
69.7/72/7%
DNAcopy [10243/4436] 63.2/64.2%
49.6/54.1%
24.2/27.8%
20.0/25.6%
33.8/36.6%
33.4/38.6%
66.4/66.8%
61.9/66.4%
72.5/72.5%
67.6/71.1%
CGHseg
[4043/1966]
54.7/56.6%
38.9/45.4%
31.1/38.8%
21.9/31.7%
38.1/41.6%
33.7/40.4%
68.0/69.6%
56.3/63.3%
74.5/75.5%
60.8/65.5%
  1. *ratio of 80% < CNV overlap segments/ratio of 5% < CNV overlap segments
  2. $:Comparison with Conrad's data, $$ Comparison with Park's data.
  3. []: represents total number of CNVs/total number of CNV deletions in original data.