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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
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

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
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

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)
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): 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 training data contains training examples with haplotag sorted images and unsorted 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.