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

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

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