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Table 1 trioPhaser results for an Ashkenazim trio, Han Chinese trio, and 50 neuroblastoma trios

From: trioPhaser: using Mendelian inheritance logic to improve genomic phasing of trios

 

Ashkenazim trio

Han Chinese trio

50 neuroblastoma trios

Genotyped variants

5,477,879

5,040,806

5,976,380

sd: 321,208

Variants phased by trioPhaser

4,640,241 (84.7%)

4,490,039 (89.1%)

4,469,479 (75.0%)

sd: 171,916

Variants phased exclusively using Mendelian inheritance logic

867,181 (18.7%)

767,992 (17.1%)

721,415 (16.1%)

sd: 54,522

Variants phased exclusively by SHAPEIT4

458,361 (9.9%)

417,138 (9.3%)

420,793 (9.4%)

sd: 15,414

Run-time (22 CPUs used)

5.8 h

5.4 h

4.4 h

  1. trioPhaser uses Mendelian inheritance in conjunction with SHAPEIT4. This hybrid approach produced a greater number of phased positions than was provided using either method exclusively. Results for the 50 neuroblastoma trios were averaged
  2. sd = Standard deviation