SV-AUTOPILOT: optimized, automated construction of structural variation discovery and benchmarking pipelines

Leung, Wai Yi; Marschall, Tobias; Paudel, Yogesh; Falquet, Laurent; Mei, Hailiang; Schönhuth, Alexander; Maoz (Moss), Tiffanie Yael

doi:10.1186/s12864-015-1376-9

BMC Genomics

Table 4 Best performing SV tool for each size class of insertion and deletion using normal and less-ideal datasets of Arabidopsis and Human Chromsome 21

From: SV-AUTOPILOT: optimized, automated construction of structural variation discovery and benchmarking pipelines

*A. Precision*
	Data type	Std Dev	Length 20–49 P (rel/str)	Length 50–99 P (rel/str)	Length 100–249 P (rel/str)	Length 250–999 P (rel/str)	Length 1 K-50 K P (rel/str)
	*Insertion*
	Human chr. 21	15	Clever	Pindel	Clever	Clever	n/a
	Human chr. 21	15	88.3/77.8	85.7/68.8	88.5/45.8	100.0/50	n/a
	Tair v.9	15	Pindel	Clever/ Pindel	Clever	Clever	n/a
	Tair v.9	15	95.0/93.2	94.3/47.4	68.1/23	66.7/55.6	n/a
	Human chr. 21	50	Pindel	Clever/Pindel	Clever	n/a	n/a
	Human chr. 21	50	87.9/75.2	83.3/55.6	66.7/17.9	n/a	n/a
	Tair v.9	50	Pindel	Clever/Pindel	Clever	Clever	n/a
	Tair v.9	50	94.9/92.7	94.6/46.2	73.9/8.3	60.0/20	n/a
	*Deletion*
	Human chr. 21	15	Clever/Pindel	Pindel	Clever/Pindel	Pindel	Breakdancer/Clever
	Human chr. 21	15	92.8/89	92.3/76.9	84.6/42.9	100/100	100/33.3
	Tair v.9	15	Pindel	Delly	Pindel	Pindel	Clever
	Tair v.9	15	94.6/94.2	100/100	89.2/90.2	87.9/88.7	68.3/58.1
	Human chr. 21	50	Clever/Pindel	Pindel	Clever/Pindel	Pindel	Breakdancer/Clever
	Human chr. 21	50	90.9/88.2	100/90	59.1/42.9	81.8/81.8	100/50
	Tair v.9	50	Pindel	Delly/Pindel	Pindel	Pindel	Clever/Pindel
	Tair v.9	50	94.5/94.3	100/90.6	86.5/86.3	89.4/89.4	69.6/61
*B. Recall*
	Data type	Std Dev	Length 20–49 R (rel/str)	Length 50–99 R (rel/str)	Length 100–249 R (rel/str)	Length 250–999 R (rel/str)	Length 1 K-50 K R (rel/str)
	*Insertion*
	Human chr. 21	15	Clever	Clever	Clever	Clever	n/a
	Human chr. 21	15	72.8	83.3	60	5.3	n/a
	Tair v.9	15	Clever	Clever	Clever	Clever	n/a
	Tair v.9	15	56.4	81.2	92.7	15.9	n/a
	Human chr. 21	50	Pindel	Clever	Clever	Clever	n/a
	Human chr. 21	50	61.8	48.6	76.7	10.5	n/a
	Tair v.9	50	Pindel	Pindel	Clever	Breakdancer	n/a
	Tair v.9	50	34.6	43	95.1	51.2	n/a
	*Deletion*
	Human chr. 21	15	Prism	Clever	Clever	Delly	Breakdancer
	Human chr. 21	15	88.1	90.9	52.6	73.7	50
	Tair v.9	15	Clever	Clever	Clever	Delly	SVDetect
	Tair v.9	15	65	82.1	89.8	93	97
	Human chr. 21	50	Prism	Prism	Clever	Breakdancer	Breakdancer
	Human chr. 21	50	85.6	72.7	63.2	73.7	50
	Tair v.9	50	Pindel	Clever	Clever	Delly	SVDetect
	Tair v.9	50	94.5	52.9	91.9	94.9	96.2

For this work, a standard deviation of 15 is considered normal while a standard deviation of 50 is considered less-ideal. Recall and Precision were two measures used to evaluate the ability of a tool to accurately predict SVs. Here the winner for each length class is provided along with the tools winning value for that category. (P = Precision; R = Recall; Std. Dev = Standard Deviation of the Insert size; n/a = no call was made by any tools tested). The Additional file 1 contains all tool performance statistics in the PDF reports. In Table 4a both ‘relaxed’ and ‘strict’ criteria (REL/STR) (see Methods) are provided for the precision measurements which indicates how accurate the tools are at making their calls. In Table 4b the scores of tool recall demonstrate how much of the SVs the tools are able to discover.

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