Table 2.

Computational approaches for Next generation trace mapping and INDEL detection

Program	Reference	INDEL discovery (%)		Validation studya	Rate (%)
		False positive	False negative
SOAP	Li et al. (27)	NR	NR	PCRb	90–100b
MAQ	Li et al. (28)	<2	35c	PCRd	100d
BWA	Li and Durbin (29)	NR	NR	ND	N/A
Pindel	Ye et al. (30)	2	20–31.4	ND	N/A
Bowtie	Langmead et al. (31)	NR	NR	ND	N/A
BFAST	Homer et al. (32)	<3	10–20	ND	N/A

NR, not reported; ND, not done; N/A, not applicable.

^aDefined as a study examining a randomly selected set of INDEL variants predicted in real humans and then measuring the confirmation rate of the predicted variants using an assay such as PCR-RFLP, PCR sequencing, microarray genotyping or similar assay.

^bFrom the Han Chinese genome sequencing project (3).

^cAt 20X coverage.

^dFrom the Korean Genome Project (7), nine coding INDELs were examined.