Skip to main content

Table 2 Parliament HS1011 summary

From: Assessing structural variation in a personal genome—towards a human reference diploid genome

Source Method Data Reference Total calls Total Loci Assembled Loci Multi source Loci Force Called Loci Solo assembled Solo forced
BreakDancer Paired End Illumina HiSeq [43] 6,474 5,520 1,740 335 194 104 82
CNVnator Read Depth Illumina HiSeq [44] 6,232 6,197 679 402 130 176 109
Crest Split Read Illumina HiSeq [45] 2,490 2,219 1,636 138 115 8 3
Delly Paired End & Split Read Illumina HiSeq [23] 4,465 3,720 1,150 323 196 109 97
Pindel Paired End Illumina HiSeq [46] 5,728 4,451 2,432 244 359 421 206
SV-STAT Reference-guided Assembly Illumina HiSeq Methods 893 892 754 90 32 9 1
Tiresias Consensus Sequences Illumina HiSeq Methods 1,354 1,347 269 36 112 76 110
Spiral Local Assembly Illumina HiSeq Methods 1,886 1,881 1,626 100 98 76 14
Illumina HiSeq Total     29,522 17,765 3,751 788 814 979 622
PBHoney Local Error and Tail Mapping PacBio RS [27] 10,759 10,340 5,883 483 0 3,792 0
SVachra Discordant Read Pairs Illumina Nextera Methods 6,208 4,785 490 454 211 96 211
aCGH + SOLiD Probe Intensity/Read Depth aCGH [25,26] 1,971 1,960 231 452 8 30 8
BioNano Irys Single-molecule Motif Mapping Irys Methods 0 343 201 142 0 41 0
Total     48,460 31,184 7,733 1,133 1,033 4,897 841
  1. Descriptions and results for each SV-detection method are provided. BioNano Irys data was used only for corroboration, not initial discovery, owing to its large size and propensity to span multiple events.