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DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data. DeepVariant is a deep learning-based variant caller that takes aligned reads (in BAM or CRAM format), produces pileup image tensors from them, classifies each tensor using a convolutional neural network, and finally reports the results in a standard VCF or gVCF file. DeepTrio is a deep learning-based trio variant caller built on top of DeepVariant. DeepTrio...

...This allows selecting the best core set of samples for model training through advanced filtering. We provide PyTorch, PyTorch Lightning and PyTorch Lightning distributed examples for each of the models to kickstart your project. Lightly requires Python 3.6+ but we recommend using Python 3.7+. We recommend installing Lightly in a Linux or OSX environment. With lightly, you can use the latest self-supervised learning methods in a modular way using the full power of PyTorch. ...