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Table 2 cnvScan implementation

From: cnvScan: a CNV screening and annotation tool to improve the clinical utility of computational CNV prediction from exome sequencing data

Program

CNV count in PIDD call set

cnvScan filtered CNV count

PIDD-causing CNV count

ExCopyDepth

769

58 (Low stringency)

4 (High stringency)

2

ExomeCopy

2782

477 (Low stringency)

180 (High stringency)

2

ExomeDepth

729

40 (Low stringency)

2 (High stringency)

2 (Low stringency)

1 (High stringency)

XHMM

151

51 (Low stringency)

49 (High stringency)

2

  1. Low stringency parameters: CNV quality score > 10, CNVQ > 10 and not reported in public CNV datasets (Sanger high resolution CNVs, 1000 Genome CNVs and high quality DGV dataset)
  2. High stringency parameters: CNV quality score > 40, CNVQ > 40 and not reported in public CNV datasets (Sanger high resolution CNVs, 1000 Genome CNVs and high quality DGV dataset)
  3. CoNIFER failed to predict PIDD-causing CNVs from these exome sets