Comprehensive characterization of copy number variation (CNV) called from array, long- and short-read data

BMC Genomics

Table 1 Summary of the CNV datasets and non-redundant CNVRs for each technology (length >500bp)

Source	CNV calling tools	Method summary	Ref.	Del.(n)	Dup.(n)	Del./Dup.
CNV regions, array	merge	-	CNVR	666	533	1.25
Illumina arrays¹	PennCNV, cnvPartition [37], Nexus [38]	I, AR	[4]	93 222	126 37	0.74 6
Affymetrix SNP 6.0	PennCNV [39], Birdsuite [40]	I, AR	[7]	73	36	2.03
CytoScan HD	apt-copynumber-cyto [41]	I, AR	our data	105	25	4.2
HapMap II genotypes	GADA [42], custom	I, genotyping	[43]	460	360	1.28
CNV regions, long reads	merge	-	CNVR	74156	23959	3.1
ECR/RR PacBio CNVs²	PBHoney [44]-v1.3.1, cm-v1.3.1/v1.3.2, assembly	intra-read discordance, soft-clipped/unmapped tails	[34]	1925	NA	NA
ECR PacBio RR PacBio Oxford Nanopore	SVIM [45]	inter-/intra-alignment signatures clustered classified	[34] [36] [46]	1235 4265 71179	799 22718 1436	1.54 0.19 49.56
CNV regions, short reads	merge	-	CNVR	12932	309	41.85
Published CNVs, >30x	svclassify [47]	SVM classifier	[47]	2502	NA	NA
Published CNVs, 50x	MetaSV [48]	ensemble of RP, SR, RD, JM, soft-clipped tails³	[48]	11748	NA	NA
1000genomes III, >7x	BreakDancer [49], CNVnator [50], Delly [14], VariationHunter [51], GenomeSTRiP [52]	RP, SR, RD, population-scale genotyping	[12]	921	6	153.5
	Delly	RP, SR		2611	122	21.4
Illumina Platinum, >30x	GRIDSS [16]	genome-wide assembly, RP, SR	[53]	2278	181	12.58
	Manta [15]	local assembly, RP, SR		2581	137	18.83

¹Selected platforms: CytoSNP850, Omni25, Omni5, OmniExpress; I, intensity; AR, allelic ratio
²ECR, Error-corrected reads; RR, Raw reads; v, blasr version; cm, custom method
³RP, read pairs; SR, split reads; RD, read depth; JM, junction mapping
Bold indicates the aggregated CNV regions based on all listed datasets for each respective technology

ISSN: 1471-2164