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DeepVariant 0.7.0
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@pichuan pichuan released this 16 Aug 01:38
· 456 commits to r0.7 since this release
v0.7.0
3c43de4

This release includes numerous performance improvements that collectively reduce the runtime of DeepVariant by about 65%.

A few highlighted changes in this release:

  • Update TensorFlow version to 1.9 built by default with Intel MKL support, speeding up call_variants runtime by more than 3x compared to v0.6.
  • The components that use TensorFlow (both inference and training) can now be run on Cloud TPUs.
  • Extensive optimizations in make_examples which result in significant runtime improvements. For example, make_examples now runs more than 3 times faster in the WGS case study than v0.6.
    • New realigner implementation (fast_pass_aligner.cc) with parameters re-tuned using Vizier for better accuracy and performance.
    • Changed window selector to use a linear decision model for choosing realignment candidates. This can be controlled by a flag. -ws_use_window_selector_model which is now on by default.
    • Many micro-optimizations throughout the codebase.
  • Added a new training case study showing how to train and fine-tune DeepVariant models.
  • Added support for CRAM files
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