samuelklee

New tools for annotation-based filtering.

9

This is a meta issue to track remaining and future work for the new tools for annotation-based filtering, which will hopefully replace VQSR. Internal developers may want to see further...

The new annotation-based filtering tools make use of the utility methods in the HDF5Utils class for writing intervals, matrices, etc. to HDF5. This class currently lives in the copynumber package,...

Updated Python and PyMC, removed TensorFlow, and added PyTorch in conda environment.

53

Copying over some discussion from Slack, with some slight modifications: > I took a quick stab at updating the environment for gCNV. Even taking out TensorFlow (assuming that the CNN...

The current implementation of VETS borrowed VQSR's logic for classifying variants into SNPs and indels, for which separate models are trained. We retained this logic to make comparisons with VQSR...

Follow up on CNN deprecation done in the update to python 3.10.

2

After the updates to the python environment made in #8561, the CNN tools are no longer functional and were deprecated. However, we may want to provide a separate environment in...