DeepSomatic:

• In this release, we are introducing FFPE_WGS_TUMOR_ONLY and FFPE_WES_TUMOR_ONLY models.
• The WGS and WGS_TUMOR_ONLY models have been retrained with all datasets described in the manuscript, tumor-in-normal and normal contamination datasets.
• Overall, we see improved generalization because of training dataset updates. We highly recommend updating to 1.9.0 for DeepSomatic analysis.

Detailed release note for DeepVariant can be found in: https://github.com/google/deepvariant/releases/tag/v1.9.0

In this release:

• Updated the doc to detail the code availability.

• No model updates.

[Updated on 2025-04-02] We are updating the WGS tumor-normal models for both r1.7.0 and r1.8.0 to ensure robustness across some rare somatic events across different cancer types.

Updates included in this release:

• DeepSomatic now has tumor-normal models to support WES and ONT.
• DeepSomatic now has FFPE-trained models for FFPE_WGS and FFPE_WES.
• DeepSomatic now supports tumor-only variant calling with Illumina WGS, ONT and PacBio.
• Improved accuracy for tumor-normal variant calling with Illumina WGS and PacBio.
• Models are trained with varying purities that improve somatic calling accuracy in cases of tumor-normal cross contamination.
• Improved runtime in make_examples and postprocess variants through code optimization.
• Models are trained with extensive training data described in this manuscript.

We are sincerely grateful to:

• Juan Carlos Mier (@jmier2) for his code and PacBio model training contributions.
• Jimin Park (@jimin001) (UCSC), Benedict Paten (@benedictpaten) (UCSC) and Mikhail Kolmogorov (@fenderglass) (NIH, NCI) for testing and providing analysis results.
• Jorge Gonzalez (@jgonzalezmendez) for helping to improve runtime.
• PacBio: Khi Pin Chua (@proteinosome), William Rowell (@williamrowell) for feedback on PacBio somatic calling.

[Updated on 2025-04-02] We are updating the WGS tumor-normal models for both r1.7.0 and r1.8.0 to ensure robustness across some rare somatic events across different cancer types.

In this release:

• We fixed a bug in call_variants that caused the step to freeze in cases where there were no examples. This bug was observed and reported in google/deepvariant#764, google/deepvariant#769, #8.
• Updated libssw library from 1.2.4 to 1.2.5.
• The same model files are used for v1.6.0 and v1.6.1 for all technologies.

• Initial Release of DeepSomatic (v1.6)
• DeepSomatic versioning will attempt to keep cadence with DeepVariant.
• Pre-trained models for Illumina and Pacific Biosciences data available.
• We are grateful to Khi Pin Chua, William Rowell (@williamrowell) and Aaron Wenger for helping us develop the PacBio model.
• We are also grateful to Jimin Park (@jimin001) (UCSC), Benedict Paten (@benedictpaten) (UCSC) and Mikhail Kolmogorov (@fenderglass) (NIH, NCI) for testing and providing analysis results.