Table 1.

Speed comparison with other methods

Method	Time (seconds)	Number of processors
BEDTools	2135.67	1
BCFTools	4776.55	1
vcfanno	2621.80	1
vcfanno	702.72	4
vcfanno	590.71	8
vcfanno	571.65	12

We compare vcfanno’s performance with BEDTools and BCFTools using 1, 4, 8, and 12 processors when annotating the ExAC dataset using nine annotation files. For all tools, we stream the output to bgzip in an effort to make the comparison as fair as possible. BCFTools can annotate only a single file at a time, so the time reported is the sum of annotating each file and sending the result to the next annotation. This cannot be piped because the input to the BCFTools “annotate” tool must first be compressed by bgzip and subsequently indexed by Tabix