Table 3. Simulation.

Filtered expected SNPs	25262
	JAGuaR	JAGuaR*	GSNAP	MapSplice 2	TopHat2
Number called SNPs	38670	44745	30371	69259	20934
Number recovered SNPs	18694	18907	19199	19789	18097
Ratio (recovered/planted)	0.74	0.75	0.76	0.78	0.72

*BWA-MEM algorithm.

All SNPs called at > = 6 bp depth.

Comparison of SNP calls between tools from a simulated dataset. PET synthetic reads were generated from a reference with 652,256 planted SNPs. These fastqs were aligned to hg19 (hg19+junctions with JAGuaR) and SNPs called. SNPs that were identified by from the alignment of at least one tool and which were in the list of planted SNPs, were considered as the filtered expected SNPs. The number of recovered SNPs are the number of SNPs out of the tool's total set that are seen in the expected list. All tools have a similar ratio. Calls from the MapSplice2 alignment show the highest number of SNPs that were not planted and calls from TopHat2 show the least.