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Table 1 Number of remaining variants per family dataset according to the filtering strategy

From: A pipeline combining multiple strategies for prioritizing heterozygous variants for the identification of candidate genes in exome datasets

Family dataset FMD exomes (N) Control dataset
(N)
PAVAR
score ≥5 (N)
Exomiser
score ≥1.46 × 10−5 (N)
VAAST
(p value ≤1)
VAAST-Phevor
(p value ≤1)
CADD
score ≥15 (N)
FATHMM
score ≤−1.5 (N)
1 3 F (1) 17 (134) 308 (1437) 40 39 15 (38) 7 (35)
T-F (29) 15 (106) 78 (296) 48 44 18 (36) 7 (34)
T (30) 10 (68) 42 (175) 27 27 12 (25) 5 (23)
2 2 F (3) 4 (58) 60 (270) 53 22 9 (18) 1 (14)
T-F (27) 9 (73) 89 (369) 146 135 12 (28) 1 (25)
T (30) 2 (34) 9 (39) 19 16 5 (13) 0 (11)
3 3 F (2) 9 (68) 151 (862) 23 23 9 (20) 1 (14)
T-F (28) 13 (92) 67 (309) 38 38 17 (25) 5 (20)
T (30) 6 (32) 24 (104) 16 16 7 (10) 1 (7)
4 3 F (0) 31 (283) 394 (2198) 54 46 34 (90) 4 (86)
T (30) 4 (34) 20 (72) 19 17 5 (14) 1 (14)
5 3 F (3) 16 (83) 93 (391) 68 22 7 (20) 1 (15)
T-F (27) 14 (113) 89 (430) 52 45 14 (35) 7 (28)
T (30) 5 (36) 18 (67) 11 9 4 (9) 1 (6)
Mean (1–5) 21 F 15.4 ± 10.21 (125) 251.5 ± 143.83 (1032) 47 ± 16.95 30.4 ± 11.33 14.8 ± 9.96 2.8 ± 2.4
T-F 12.75 ± 2.63 (96) 85 ± 28.66 (351) 71 ± 50.35 65.5 ± 46.44 13.5 ± 4.38 5.0 ± 2.44
T 5.2 ± 2.97 (51) 31 ± 13.94 (155) 28.2 ± 5.81 5.81 ± 6.44 6.60 ± 2.87 1.6 ± 1.74
  1. All variants with a MAF >0.001 were discarded. Setting for each software threshold is described in the “Material and methods” section
  2. p values for VAAST and Phevor were not corrected since they were used as thresholds according to the user’s guide
  3. F family controls exome dataset, T-F in-house controls exome dataset without family control dataset, T in-house and family control datasets