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Simplified DeepVariant PacBio by introducing approximate haplotagging. This means PacBio users who run DeepVariant no longer need to run DeepVariant+WhatsHap+DeepVariant. See PacBio case study for more information.
For Illumina WGS and WES, we add an additional feature of read insert size (insert_size) . This reduces errors by 4-10% for Illumina WGS and WES model. Thanks @lucasbrambrink for implementing this feature.
Reduced the runtime of the postprocess_variants step by 10-30%. Thanks @MosheWagner for optimizing the code.
Included experimental code which explores use of Keras for model architecture. This is not used in production methods, but may be informative to developers seeking examples of Keras applied to similar problems. Thanks @wkwan and @paulinesho for their contributions.
We did not include OpenVINO by default in the Docker images we released. Users can still build their own Docker images with the option turned on as needed.
Updated 2022-10-17: We have released an Illumina RNA-seq model and added an RNA-seq case study.