Table 5  Comparisons of ibd inference using using ibd_haplo and using fastIBD
Program:True-positive ibd inferenceFalse-positive ibd inference
InputScoringLD level γLD level γ
0.00.050.11.00.00.050.11.0
ibd_haplo:All ibd69.374.577.080.917.28.53.80.1
Hap dataBtw ibd69.874.577.581.3
ibd_haplo:All ibd53.457.659.861.712.16.53.40.1
Gen dataBtw ibd46.149.752.353.3
fastIBD:Strict31.441.246.456.90.60.70.81.0
100 baseLoose56.364.668.982.92.22.32.34.0
fastIBD:Strict41.551.456.971.70.70.90.91.5
1000 baseLoose66.573.377.690.43.43.13.18.9
  • Results are shown at decreasing levels of LD (that is, increasing γ), and are tabulated as percentages over the 6913 markers over all 500 pairs of individuals. The ibd haplo program was run for both haplotypic (Hap.) and genotypic data (Gen.). For scoring ibd all states involving any ibd were scored (All ibd), as in Table 3, and then also only between-individual ibd was scored (Btw ibd), since fastIBD does not seek within-individual ibd. The fastIBD program was run using only the same 100 individuals for the BEAGLE imputation and phasing step as used in ibd haplo, and then also using an additional 900 individuals for a base sample of 1000. The ibd was scored using a strict (10−10) threshold and a looser threshold (10−6).