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deeptrio-details-training-data.md

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DeepTrio training data

WGS models

version Replicates #examples
Child model
1.1.0 4 HG001/NA12891/NA12892 trios
7 HG005/HG006/HG007 trios
3 HG002/HG003/HG004 trios		 566,589,652(1)
1.2.0 (Same model as 1.1.0)
1.3.0 (Same model as 1.1.0)
1.4.0 4 HG001/NA12891/NA12892 trios
7 HG005/HG006/HG007 trios
3 HG002/HG003/HG004 trios		 704,228,446
1.5.0 (6)4 HG001, 3 HG002, 3 HG003, 3 HG004, 7 HG005, 6 HG006, 6 HG007, 4 NA12891, 4 NA12892 704,228,358
1.6.0 (6)4 HG001, 3 HG002, 3 HG003, 3 HG004, 7 HG005, 6 HG006, 6 HG007, 4 NA12891, 4 NA12892 704,394,556
Parent model
1.1.0 7 HG005/HG006/HG007 trios
3 HG002/HG003/HG004 trios		 315,847,934
1.2.0 (Same model as 1.1.0)
1.3.0 (Same model as 1.1.0)
1.4.0 7 HG005/HG006/HG007 trios
3 HG002/HG003/HG004 trios		 457,374,516
1.5.0 (6)3 HG002, 3 HG003, 3 HG004, 7 HG005, 6 HG006, 6 HG007 457,374,464
1.6.0 (6)2 HG001, 3 HG002, 3 HG003, 3 HG004, 7 HG005, 6 HG006, 6 HG007, 2 NA12891, 2 NA12892 457,420,038

WES models

version Replicates #examples
Child model
1.1.0 27 HG001/NA12891/NA12892 trios
6 HG005/HG006/HG007 trios
7 HG002/HG003/HG004 trios		 18,002,596
1.2.0 (Same model as 1.1.0)
1.3.0 (Same model as 1.1.0)
1.4.0 27 HG001/NA12891/NA12892 trios
6 HG005/HG006/HG007 trios
6 HG002/HG003/HG004 trios		 27,776,416
1.5.0 (6)9 HG001, 7 HG002, 7 HG003, 7 HG004, 8 HG005, 8 HG006, 8 HG007, 9 NA12891, 9 NA12892 27,791,954
1.6.0 (6)9 HG001, 7 HG002, 7 HG003, 7 HG004, 8 HG005, 8 HG006, 8 HG007, 9 NA12891, 9 NA12892 27,783,324
Parent model
1.1.0 6 HG005/HG006/HG007 trios
6 HG002/HG003/HG004 trios		 4,131,018
1.2.0 (Same model as 1.1.0)
1.3.0 (Same model as 1.1.0)
1.4.0 6 HG005/HG006/HG007 trios
6 HG002/HG003/HG004 trios		 13,036,995
1.5.0 (6)6 HG002, 6 HG003, 6 HG004, 8 HG005, 8 HG006, 8 HG007 13,036,998
1.6.0 (6)6 HG002, 6 HG003, 6 HG004, 8 HG005, 8 HG006, 8 HG007 13,039,595

PACBIO models(2)(3)

version Replicates #examples
Child model
1.1.0 1 HG005/HG006/HG007 trio
8 HG002/HG003/HG004 trios		 397,610,700
1.2.0 1 HG005/HG006/HG007 trio
8 HG002/HG003/HG004 trios		 406,893,180(4)
1.3.0 2 HG005/HG006/HG007 trio
10 HG002/HG003/HG004 trios		 539,382,124(5)
1.4.0 (Same model as 1.3.0)
1.6.0 9 HG002, 5 HG003, 5 HG004, 1 HG005, 1 HG006, 1 HG007 890,016,014(5)
Parent model
1.1.0 1 HG005/HG006/HG007 trio
8 HG002/HG003/HG004 trios		 386,418,918
1.2.0 1 HG005/HG006/HG007 trio
8 HG002/HG003/HG004 trios		 392,749,204(4)
1.3.0 2 HG005/HG006/HG007 trio
10 HG002/HG003/HG004 trios		 533,353,050(5)
1.4.0 (Same model as 1.3.0)
1.6.0 9 HG002, 5 HG003, 5 HG004, 1 HG005, 1 HG006, 1 HG007 838,515,085(5)

ONT models(2)(3)

version Replicates #examples
1.6.0 1 HG002, 1 HG002, 1 HG004 50,249,704(5)
Parent model
1.6.0 1 HG002, 1 HG002, 1 HG004 99,675,190(5)
(1): We include HG002/HG003/HG004 for training WGS
model, but only using examples from the region of NIST truth confident region
v4.2 subtracting v3.3.2.

(2): We use the entire HG002/HG003/HG004 trio for PacBio model training.

(3): PacBio and ONT training data contains training examples with haplotag sorted images.

(4): In v1.2.0, we updated the NIST truth versions we used for training.

(5): In v1.3.0, we included PacBio Sequel II Chemistry v2.2 data in the training dataset. And we updated to NIST truth version to v4.2.1.

(6): Starting in v1.5.0, for clarity, we report the number of unique BAM files used. Note that this doesn't mean all the trios were paired together to produce training data.