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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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Genome Medicine

ISSN: 1756-994X

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