Table 2.

Summary of CNV runs on different callers

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

BI Broad Institute, WUGSC Washington University Genome Sequencing Center, BI-GIH Broad Institute Gujarati Indians in Houston, Texas

^aO denotes that a caller was run on a given dataset

^b– denotes that a caller was not run on a given dataset

^cIndicates data comprising 48 samples, 16 samples from each of the three capture kit samples