Table 2.

Benchmark results of ParseCNV2 on various Genomic Data.

RUN	Cases	Controls	CPU	TIME (h:mm:ss)	MEM (kbytes)	Del Case Enrich (Pass + Fail)	Del Control Enrich (Pass + Fail)	Dup Case Enrich (Pass + Fail)	Dup Control Enrich (Pass + Fail)
ParseCNV2 Array	5	5	85%	0:00:11	280,888	0 + 0	0 + 0	0 + 0	0 + 0
ParseCNV2 Array (550k)	785	1110	94%	0:01:29	280,888	49 + 11	31 + 5	33 + 2	37 + 4
ParseCNV2 Array (2.5 M)	700	797	96%	0:06:35	280,716	143 + 1	190 + 4	124 + 13	73 + 4
ParseCNV2 WES	758	1344	97%	0:06:29	280,896	42 + 2	2 + 0	154 + 25	49 + 3
ParseCNV2 WGS	205	689	96%	0:56:43	758,776	556 + 17	455 + 9	293 + 13	353 + 14
ParseCNV(original) Array	5	5	80%	0:0:16	280,616	0 + 0	0 + 0	0 + 0	0 + 0
ParseCNV(original) Array (550k)	785	1110	93%	0:0:32	280,620	17 + 39	3 + 27	17 + 13	9 + 31
ParseCNV(original) Array (2.5 M)	700	797	97%	0:1:49	789,468	66 + 56	18 + 148	41 + 86	24 + 42
ParseCNV(original) WES	758	1344	98%	0:5:19	991,372	0 + 45	0 + 17	0 + 179	0 + 49
ParseCNV(original) WGS	205	689	98%	1:06:11	14,440,980	0 + 458	0 + 335	0 + 145	0 + 115
Plink2 UKB AguirreEtAl	6564	15,480	99%	0:34:21	104,528	0	55	0	2
ParseCNV2 UKB AguirreEtAl	6564	15,480	99%	2:32:20	973,120	17 + 8	83 + 8	8 + 4	22 + 2
Plink2 CNVMAP2 CAG INTERNAL	20,637	48,314	99%	3:51:17	298,496	4567	980	2707	570
ParseCNV2 CNVMAP2 CAG INTERNAL	20,637	48,314	99%	33:51:57	14,907,708	777 + 2	871 + 1	801 + 0	680 + 3
CNVRanger 1KG qt	2504 values		98%	0:46:36	2,629,344	901
ParseCNV2 1KG cc	767	1,737	98%	0:23:59	871,864	241 + 81	170 + 88	256 + 28	174 + 16
ParseCNV2 1KG qt	2504 values		97%	0:27:18	872,832	324 + 96	390 + 112	276 + 81	256 + 83
ParseCNV(original) 1KG cc	767	1,737	99%	0:14:08	3,923,728	239 + 70	32 + 232	193 + 59	123 + 83
ParseCNV(original) 1KG qt	2504 values		91%	0:46:15	4,409,288	398	470	342	313
Plink2 1KG cc	767	1737	99%	0:00:22	705,608	140	55	155	36