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@kathyxchen kathyxchen released this 30 Jul 15:59
· 154 commits to master since this release
0.4.0
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Learn about vigilant mode.

Updates:

  • Variant effect prediction: adjustments made to variant centering and strand-specific sequence handling so that the sequence context fetched for a variant matches the implementation for code associated with DeepSEA and SeqWeaver (https://hb.flatironinstitute.org/asdbrowser/help, https://github.com/FunctionLab/expecto)
  • Predicting on sequences accepts BED file as input
  • Add compatibility with Lua-trained DeepSEA and SeqWeaver models (converted to PyTorch) - models themselves will be officially released through the ASD browser on HumanBase in the coming weeks.
  • Simplified the prediction handlers output for variant effect prediction - sequences where the reference allele doesn't match the reference genome are no longer diverted to a new file. Rather, a column has been added ref_match that denotes whether the allele matches or not.

Bug fixes:

  • Predicting on sequences: previously did not output anything if N < batch size
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