Table 1. Benchmark of three SNP database systems.

Each dataset is loaded into an empty database. The timings are wall clock times averaged over three runs for the HapMap and two runs for the second data set.

Tasks	units	dbVOR	SNPpy	TheSNPpit
load all HapMap data 225@620K	h:m:s	00:09:08	00:10:38	00:00:22
export all genotypes to map/ped	h:m:s	00:04:59	00:04:04	00:00:07
export chromosome 1 to map/ped	h:m:s	00:00:25	00:00:42	00:00:07
database size	MB	522	9,086	73
load all data 5509@581K	h:m:s	01:10:04	03:58.06	00:10:14
export all genotypes to map/ped	h:m:s	02:58:04	01:29:16	00:01:16
export chromosome 1 to map/ped	h:m:s	00:22:37	00:30:21	00:00:19
database size	MB	8,198	201,326	868