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504df64
Remove ONT duplex from case-study
kishwarshafin May 8, 2025
d70da8e
Update metrics page of DV, DS, Pang-DV, DT.
kishwarshafin May 9, 2025
7c9c264
Update all case-studies for 1.9 release
kishwarshafin May 9, 2025
5177f6e
Update all DeepTrio case-studies for 1.9 release (including metrics)
lucasbrambrink May 12, 2025
9f589b9
Update case studies for 1.9
kishwarshafin May 12, 2025
43283f7
Update training docs for 1.9 release
kishwarshafin May 13, 2025
d65a503
Remove duplex case-study from readme.
kishwarshafin May 16, 2025
6fc7e0f
Added permissions to small_model in DeepTrio
kishwarshafin May 16, 2025
ea4de59
Update deeptrio-details.md
parsaeskandar Aug 29, 2025
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1 change: 1 addition & 0 deletions Dockerfile.deeptrio
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Expand Up @@ -191,6 +191,7 @@ ADD https://storage.googleapis.com/deepvariant/models/DeepTrio/${VERSION_DEEPTRI
WORKDIR /opt/smallmodels/deeptrio/wgs/child/variables
ADD https://storage.googleapis.com/deepvariant/models/DeepTrio/${VERSION_DEEPTRIO}/smallmodels/deeptrio.wgs_child.smallmodel/variables/variables.data-00000-of-00001 \
https://storage.googleapis.com/deepvariant/models/DeepTrio/${VERSION_DEEPTRIO}/smallmodels/deeptrio.wgs_child.smallmodel/variables/variables.index ./
RUN chmod -R +r /opt/smallmodels/deeptrio/wgs/child/*


WORKDIR /opt/smallmodels/deeptrio/wgs/parent
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3 changes: 1 addition & 2 deletions README.md
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Expand Up @@ -19,8 +19,7 @@ DeepVariant supports germline variant-calling in diploid organisms.
* PacBio HiFi data
[PacBio case study](docs/deepvariant-pacbio-model-case-study.md).
* Oxford Nanopore R10.4.1
[Simplex case study](docs/deepvariant-ont-r104-simplex-case-study.md),
[Duplex case study](docs/deepvariant-ont-r104-duplex-case-study.md).
[Simplex case study](docs/deepvariant-ont-r104-simplex-case-study.md).
* Complete Genomics
[T7 case study](docs/deepvariant-complete-t7-case-study.md);
[G400 case study](docs/deepvariant-complete-g400-case-study.md).
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1 change: 0 additions & 1 deletion docs/README.md
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Expand Up @@ -9,7 +9,6 @@
* [DeepVariant exome case study](deepvariant-exome-case-study.md)
* [DeepVariant PacBio case study](deepvariant-pacbio-model-case-study.md)
* [DeepVariant ONT R10.4 simplex case study](deepvariant-ont-r104-simplex-case-study.md)
[DeepVariant ONT R10.4 duplex case study](deepvariant-ont-r104-duplex-case-study.md)
* [DeepVariant hybrid (PacBio and Illumina) case study](deepvariant-hybrid-case-study.md)
* [DeepVariant Complete Genomics T7 case study](deepvariant-complete-t7-case-study.md)
* [DeepVariant Complete Genomics G400 case study](deepvariant-complete-g400-case-study.md)
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5 changes: 5 additions & 0 deletions docs/deeptrio-details-training-data.md
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Expand Up @@ -18,6 +18,7 @@ Parent model |
1.4.0 | 7 HG005/HG006/HG007 trios <br> 3 HG002/HG003/HG004 trios | 457,374,516
1.5.0 | <sup>[(6)](#vfootnote6)</sup>3 HG002, 3 HG003, 3 HG004, 7 HG005, 6 HG006, 6 HG007 | 457,374,464
1.6.0 | <sup>[(6)](#vfootnote6)</sup>2 HG001, 3 HG002, 3 HG003, 3 HG004, 7 HG005, 6 HG006, 6 HG007, 2 NA12891, 2 NA12892 | 457,420,038
1.9.0 | <sup>[(6)](#vfootnote6)</sup>2 HG001, 3 HG002, 3 HG003, 3 HG004, 7 HG005, 6 HG006, 6 HG007, 2 NA12891, 2 NA12892 | 457,420,038

### WES models

Expand All @@ -37,6 +38,7 @@ Parent model |
| 1.4.0 | 6 HG005/HG006/HG007 trios <br> 6 HG002/HG003/HG004 trios | 13,036,995 |
| 1.5.0 | <sup>[(6)](#vfootnote6)</sup>6 HG002, 6 HG003, 6 HG004, 8 HG005, 8 HG006, 8 HG007 | 13,036,998 |
| 1.6.0 | <sup>[(6)](#vfootnote6)</sup>6 HG002, 6 HG003, 6 HG004, 8 HG005, 8 HG006, 8 HG007 | 13,039,595 |
| 1.9.0 | <sup>[(6)](#vfootnote6)</sup>6 HG002, 6 HG003, 6 HG004, 8 HG005, 8 HG006, 8 HG007 | 13,039,595 |



Expand All @@ -56,13 +58,16 @@ Parent model |
| 1.3.0 | 2 HG005/HG006/HG007 trio <br>10 HG002/HG003/HG004 trios | 533,353,050<sup>[(5)](#vfootnote5)</sup> |
| 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<sup>[(5)](#vfootnote5)</sup> |
| 1.9.0 | 9 HG002, 5 HG003, 5 HG004, 1 HG005, 1 HG006, 1 HG007 | 607,118,560<sup>[(5)](#vfootnote5)</sup> |

### ONT models<sup>[(2)](#vfootnote2)</sup><sup>[(3)](#vfootnote3)</sup>
| version | Replicates | #examples |
| ------------ | ---------------------------------- | ----------- |
| 1.6.0 | 1 HG002, 1 HG002, 1 HG004 | 50,249,704<sup>[(5)](#vfootnote5)</sup> |
| Parent model | | |
| 1.6.0 | 1 HG002, 1 HG002, 1 HG004 | 99,675,190<sup>[(5)](#vfootnote5)</sup> |
| 1.9.0 | 5 HG002, 5 HG004, 4 HG005, 4 HG006, 4 HG007 | 607,118,560<sup>[(5)](#vfootnote5)</sup> |

<a name="vfootnote1">(1)</a>: 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.
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2 changes: 1 addition & 1 deletion docs/deeptrio-details.md
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Expand Up @@ -66,7 +66,7 @@ chromosome (e.g. for chromosomeX, only the mother and son samples and for
chromosomeY only the father and son samples).

If needed, DeepTrio can be built from source. For more details please refer to
[Building DeeepTrio](deeptrio-build-test.md).
[Building DeepTrio](deeptrio-build-test.md).

## DeepTrio Input assumptions

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38 changes: 19 additions & 19 deletions docs/deeptrio-pacbio-case-study.md
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Expand Up @@ -85,7 +85,7 @@ is run as a separate command.
mkdir -p output
mkdir -p output/intermediate_results_dir

BIN_VERSION="1.8.0"
BIN_VERSION="1.9.0"

sudo apt -y update
sudo apt-get -y install docker.io
Expand Down Expand Up @@ -221,13 +221,13 @@ As a result we should get the following output:
```bash
Checking: /output/HG002_trio_merged.vcf.gz
Family: [HG003 + HG004] -> [HG002]
188 non-pass records were skipped
Concordance HG002: F:166225/169750 (97.92%) M:166415/168977 (98.48%) F+M:159575/164659 (96.91%)
126 non-pass records were skipped
Concordance HG002: F:173615/180788 (96.03%) M:174179/180845 (96.31%) F+M:165688/177112 (93.55%)
Sample HG002 has less than 99.0 concordance with both parents. Check for incorrect pedigree or sample mislabelling.
0/188437 (0.00%) records did not conform to expected call ploidy
176829/188437 (93.84%) records were variant in at least 1 family member and checked for Mendelian constraints
10143/176829 (5.74%) records had indeterminate consistency status due to incomplete calls
6722/176829 (3.80%) records contained a violation of Mendelian constraints
0/191837 (0.00%) records did not conform to expected call ploidy
185941/191837 (96.93%) records were variant in at least 1 family member and checked for Mendelian constraints
7334/185941 (3.94%) records had indeterminate consistency status due to incomplete calls
12647/185941 (6.80%) records contained a violation of Mendelian constraints
```

### Benchmark variant calls against 4.2.1 truth set with hap.py
Expand Down Expand Up @@ -289,22 +289,22 @@ sudo docker run \
```
Benchmarking Summary for HG002:
Type Filter TRUTH.TOTAL TRUTH.TP TRUTH.FN QUERY.TOTAL QUERY.FP QUERY.UNK FP.gt FP.al METRIC.Recall METRIC.Precision METRIC.Frac_NA METRIC.F1_Score TRUTH.TOTAL.TiTv_ratio QUERY.TOTAL.TiTv_ratio TRUTH.TOTAL.het_hom_ratio QUERY.TOTAL.het_hom_ratio
INDEL ALL 11256 11213 43 23405 84 11635 32 45 0.996180 0.992863 0.497116 0.994519 NaN NaN 1.561710 2.151675
INDEL PASS 11256 11213 43 23405 84 11635 32 45 0.996180 0.992863 0.497116 0.994519 NaN NaN 1.561710 2.151675
SNP ALL 71333 71305 28 108561 21 37160 14 7 0.999607 0.999706 0.342296 0.999657 2.314904 1.742256 1.715978 1.772847
SNP PASS 71333 71305 28 108561 21 37160 14 7 0.999607 0.999706 0.342296 0.999657 2.314904 1.742256 1.715978 1.772847
INDEL ALL 11256 11214 42 23119 78 11356 32 40 0.996269 0.993369 0.491198 0.994817 NaN NaN 1.561710 2.075045
INDEL PASS 11256 11214 42 23119 78 11356 32 40 0.996269 0.993369 0.491198 0.994817 NaN NaN 1.561710 2.075045
SNP ALL 71333 71310 23 109529 18 38126 9 9 0.999678 0.999748 0.348090 0.999713 2.314904 1.724732 1.715978 1.611481
SNP PASS 71333 71310 23 109529 18 38126 9 9 0.999678 0.999748 0.348090 0.999713 2.314904 1.724732 1.715978 1.611481

Benchmarking Summary for HG003:
Type Filter TRUTH.TOTAL TRUTH.TP TRUTH.FN QUERY.TOTAL QUERY.FP QUERY.UNK FP.gt FP.al METRIC.Recall METRIC.Precision METRIC.Frac_NA METRIC.F1_Score TRUTH.TOTAL.TiTv_ratio QUERY.TOTAL.TiTv_ratio TRUTH.TOTAL.het_hom_ratio QUERY.TOTAL.het_hom_ratio
INDEL ALL 10628 10577 51 23776 77 12634 33 43 0.995201 0.993089 0.531376 0.994144 NaN NaN 1.748961 2.332224
INDEL PASS 10628 10577 51 23776 77 12634 33 43 0.995201 0.993089 0.531376 0.994144 NaN NaN 1.748961 2.332224
SNP ALL 70166 70143 23 117125 35 46898 13 9 0.999672 0.999502 0.400410 0.999587 2.296566 1.57963 1.883951 1.685873
SNP PASS 70166 70143 23 117125 35 46898 13 9 0.999672 0.999502 0.400410 0.999587 2.296566 1.57963 1.883951 1.685873
INDEL ALL 10628 10575 53 23560 71 12427 36 34 0.995013 0.993623 0.527462 0.994317 NaN NaN 1.748961 2.321257
INDEL PASS 10628 10575 53 23560 71 12427 36 34 0.995013 0.993623 0.527462 0.994317 NaN NaN 1.748961 2.321257
SNP ALL 70166 70149 17 118416 32 48186 8 11 0.999758 0.999544 0.406921 0.999651 2.296566 1.576658 1.883951 1.697684
SNP PASS 70166 70149 17 118416 32 48186 8 11 0.999758 0.999544 0.406921 0.999651 2.296566 1.576658 1.883951 1.697684

Benchmarking Summary for HG004:
Type Filter TRUTH.TOTAL TRUTH.TP TRUTH.FN QUERY.TOTAL QUERY.FP QUERY.UNK FP.gt FP.al METRIC.Recall METRIC.Precision METRIC.Frac_NA METRIC.F1_Score TRUTH.TOTAL.TiTv_ratio QUERY.TOTAL.TiTv_ratio TRUTH.TOTAL.het_hom_ratio QUERY.TOTAL.het_hom_ratio
INDEL ALL 11000 10954 46 24235 70 12701 29 36 0.995818 0.993931 0.524077 0.994874 NaN NaN 1.792709 2.351344
INDEL PASS 11000 10954 46 24235 70 12701 29 36 0.995818 0.993931 0.524077 0.994874 NaN NaN 1.792709 2.351344
SNP ALL 71659 71617 42 116988 22 45260 11 7 0.999414 0.999693 0.386877 0.999554 2.310073 1.633809 1.878340 1.626369
SNP PASS 71659 71617 42 116988 22 45260 11 7 0.999414 0.999693 0.386877 0.999554 2.310073 1.633809 1.878340 1.626369
INDEL ALL 11000 10952 48 23981 61 12453 30 27 0.995636 0.994709 0.519286 0.995172 NaN NaN 1.792709 2.328987
INDEL PASS 11000 10952 48 23981 61 12453 30 27 0.995636 0.994709 0.519286 0.995172 NaN NaN 1.792709 2.328987
SNP ALL 71659 71622 37 118880 18 47151 6 8 0.999484 0.999749 0.396627 0.999616 2.310073 1.620779 1.878340 1.616919
SNP PASS 71659 71622 37 118880 18 47151 6 8 0.999484 0.999749 0.396627 0.999616 2.310073 1.620779 1.878340 1.616919
```
4 changes: 2 additions & 2 deletions docs/deeptrio-quick-start.md
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Expand Up @@ -32,7 +32,7 @@ documentation on how to build.
### Get Docker image

```bash
BIN_VERSION="1.8.0"
BIN_VERSION="1.9.0"

sudo apt -y update
sudo apt-get -y install docker.io
Expand Down Expand Up @@ -338,7 +338,7 @@ INDEL PASS 2 2 0 2 0 0
[BAM]: http://genome.sph.umich.edu/wiki/BAM
[BWA]: https://academic.oup.com/bioinformatics/article/25/14/1754/225615/Fast-and-accurate-short-read-alignment-with
[docker build]: https://docs.docker.com/engine/reference/commandline/build/
[Dockerfile]: https://github.com/google/deepvariant/blob/r1.8/Dockerfile.deeptrio
[Dockerfile]: https://github.com/google/deepvariant/blob/r1.9/Dockerfile.deeptrio
[FASTA]: https://en.wikipedia.org/wiki/FASTA_format
[VCF]: https://samtools.github.io/hts-specs/VCFv4.3.pdf
[run_deeptrio.py]: ../scripts/run_deeptrio.py
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