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Table 6 Results by the application of selection parameters and their thresholds on simulated datasets

From: GATK hard filtering: tunable parameters to improve variant calling for next generation sequencing targeted gene panel data

 

TV

N (%)

FV

N (%)

Variant selected by hard filtering %

HC dataset

 Homo SNVs

   Overall

2,382 (66.6)

1,195 (33.4)

93.9

   Selected

2,238 (98.6)

31 (1.3)

 

 Het SNVs

   Overall

87,361 (99.8)

177 (0.2)

98.6

   Selected

86,166 (99.9)

24 (0.03)

 

 Homo indels

   Overall

54 (0.12)

43,871 (99.8)

27.7

   Selected

15 (75)

5 (25)

 

 Het indels

   Overall

17.305 (45.8)

20,410 (54.1)

84.6

   Selected

14,646 (94)

935 (6)

 

LC dataset

 Homo SNVs

   Overall

2,084 (12.38)

14,721 (87.6)

96.9

   Selected

2,020 (92.2)

171 (7.8)

 

 Het SNVs

   Overall

95,119 (97.6)

2,322 (2.3)

99.4

   Selected

94,602 (99.9)

80 (0.08)

 

 Homo indels

   Overall

154 (0.4)

45623 (99.6)

100

   Selected

154 (0.4)

45623 (99.6)

 

 Het indels

   Overall

7,502 (17.6)

34,889 (82.3)

43

   Selected

3,226 (99.1)

27 (0.8)

 
  1. % have to be intended as the percentage of unfiltered variants for “overall”calls and as the percentage of alterations which were not filtered out in the hard filtering process for “selected”calls; % of selection indicates the amount of variants selected from the total callset. TV true variants, FV false variants