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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