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

BMC Genomics

Table 2 Parliament HS1011 summary

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

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.

ISSN: 1471-2164