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Table 2 Summary of CNV runs on different callers

From: Assessing the reproducibility of exome copy number variations predictions

Dataset XHMM CoNIFER CONTRA EXCAVATOR
 BI (167) Oa O b O
 WUGSC (116) O O O
 BI GIH (48) O O O O
 ClinSeq® (54) O O O O
Sample size analysis (ClinSeq® in triplicates by random sampling)
 10 O O O
 30 O O O
 75 O O O
 100 O O O
 300 O O O
Capture kit analysis (48 samples from ClinSeq® in triplicates by random sampling)
 SS HAE O O O
 SS ICGC O O O
 TruSeq v2 O O O
 Mix capturec O O O
  1. BI Broad Institute, WUGSC Washington University Genome Sequencing Center, BI-GIH Broad Institute Gujarati Indians in Houston, Texas
  2. aO denotes that a caller was run on a given dataset
  3. b– denotes that a caller was not run on a given dataset
  4. cIndicates data comprising 48 samples, 16 samples from each of the three capture kit samples
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