VCF observer: a user-friendly software tool for preliminary VCF file analysis and comparison

BMC Bioinformatics

Table 2 Performance test results showing times (in seconds (s)) for various operations performed by VCF Observer

	1 k	10 k	100 k	1 M	10 M
Generating venn diagram (s)	0.12	0.15	0.96	9.95	120.17
Generating precision–recall plot (s)	0.05	0.13	0.86	8.6	101.43
Applying PASS filtering (s)	0.01	0.05	0.45	4.4	49.1
Applying BED filtering (s)	0.73	0.77	1.23	5.95	63.5
Applying BED filtering* (s)	0.62	0.72	1.78	12.6	137.09

Each row contains the average running time of 10 runs of a particular test performed with various input file sizes. There are five tests: “Generating Venn Diagram”, “Generating Precision–Recall Plot”, “Applying PASS Filtering”, and 2 instances of “Applying BED Filtering”. *The latter BED filtering test was performed using an earlier implementation of our genomic regions-based VCF filtering algorithm to demonstrate the effectiveness of the optimization described in Implementation. k: 1000, M: 1,000,000

ISSN: 1471-2105