github.com/broadinstitute/gatk-sv-ploidy/Ploidy

Automatic Tools and Workflows
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gatk-sv-ploidy

Whole-genome aneuploidy detection from binned read counts with optional
per-site allele fraction evidence.

This package is intended for use with the
gatk-sv pipeline.

The package implements a baseline-aware pipeline:

  1. preprocess raw depth and optionally build per-site allele fraction tensors,
  2. optionally classify each sample’s autosomal baseline CN as CN1, CN2, CN3,
    or CN4,
  3. fit a Pyro-based Bayesian copy-number model,
This is a companion discussion topic for the original entry at github.com/broadinstitute/gatk-sv-ploidy/Ploidy