Table 4.

Evaluation of Dindel on paired-end 50-bp Illumina GAII data for a targeted resequencing study of a 3.8-kb region on chromosome 11

Capillary data and PCR short-read data were available for 107 samples corresponding to 96 individuals. The capillary data revealed two variable indel sites in this region. Among the 107 × 2 = 214 sites in the 107 samples, N = 89 contained at least one copy of the non-reference variant.

^aThe second column shows how many of the 89 were detected from the short-read data.

^bShows how many indels at sites other than the two variable sites were called from the short-read data, representing likely false calls.

^cGenotype concordance and the type of genotype miscall made by Dindel.

^d“Ref as het,” the capillary data indicated no non-reference variant, while the Dindel call was a heterozygote; “Het as hom-non-ref,” a capillary heterozygote was called as a non-reference homozygote by Dindel. “Hom-nonref as het,” a capillary homozygote for the non-refererence allele was called as a heterozygote by Dindel.