Table 2 (abstract P41). Example of summary statistics comparing Atlas genotype calls with differing allele fraction thresholds with GATK calls.

Genotype

GATK

ATLAS (ORIGINALS)

ATLAS

DP>=10

0.25<0/1>0.75

ATLAS

DP>=10

0.1<0/1>0.9

ATLAS

DP>=10

0.1<0/1>0.75

0/0

1,793,394,356

1,788,668,240

1,778,668,240

1,778,668,240

1,778,668,240

0/1

138,744,203

69,153,666

112,165,710

147,763,797

124,056,267

1/1

79,407,733

60,398,312

73,417,546

49,710,016

73,423,295

Het / hom

1.75

1.14

1.53

2.97

1.69

Total

2,011,546,292

1,908,220,218

1,964,251,496

1,976,142,053

1,976,147,802

Concordant Genotypes

GATK + ATLAS (ORIGINALS)

GATK + ATLAS (0.25<0/1>0.75)

GATK + ATLAS (0.1<0/1>0.9)

GATK + ATLAS (0.1<0/1>0.75)

0/0

914,737,638

1,021,734,445

1,050,682,661

1,049,337,470

0/1

39,133,931

72,422,398

74,278,418

75,570,661

1/1

17,017,045

45,077,505

33,993,884

45,368,697

Het/hom

2.30

1.61

2.19

1.67

Total

970,888,614

1,139,234,348

1,158,954,963

1,170,276,828