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Table 1 The key features of 12 methods

From: A systematic evaluation of copy number alterations detection methods on real SNP array and deep sequencing data

MethodWindow sizeNormalizationSegmentationContaminationPloidy
BICseqManualRatio centralization (built-in)Bayesian information criterionNoNo
CNVnormManualGC, smoothing, Ratio centralization (built-in)Circular binary segmentationYesYes
FREECCV and Poisson distributionGC, mappability, Ratio centralization (built-in)LASSO and dynamic programmingYesNo
CNV_seqGaussian Ratio and Geary-Hinkley transformationRatio centralization (manual)Consecutive Overlapping windowsNoNo
rSWseqNo needRatio centralization (manual)Smith-WatermanNoNo
VarscanFixed length broke by the gap and significant changeRatio centralization (manual)Circular binary segmentationNoNo
CNVnatorManualGCMean shift algorithmNoNo
ReadDepthNegative binomialGC, mappabilityCircular binary segmentationNoNo
RDXplorerManualGCEvent wise testingNoNo
GPHMMHMMYesYesa
GAPCircular binary segmentationYesYes
OncoSNPHMMYesYesa
  1. aThey don’t directly give the ploidy estimation in the output file, but through baseline shift and exact copy number results the ploidy is indirectly known