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First cut of VariantWorks SDK!

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@tijyojwad tijyojwad released this 08 Jun 20:04
· 182 commits to master since this release

Introducing VariantWorks SDK - python framework to simplify the development of deep learning powered variant and consensus calling from reads.

Highlights of first cut

  1. Encoder - Read pileup encoder with support for read, base quality, mapping quality data, and reference and allele proposal encodings.
  2. I/O - VCF reader for parsing true and false positive variant samples for training.
  3. Data Loader - NeMo wrapped data loader implementations for online and offline data loading/encoding.
  4. Samples - A trainer/evaluator app for simple SNP zygosity calling using a CNN.

More details available at https://clara-parabricks.github.io/VariantWorks/