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DeepVariant 0.6.0

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@pichuan pichuan released this 10 Apr 21:54
· 12 commits to r0.6 since this release

This release has a new WGS model that has major accuracy improvement on PCR+ data. We also released a new WES model that has some minor accuracy improvement.

A few important changes in this release:

  1. Changes in the training data for the WGS model:
    • Addition:
      • 3 replicates of HG001 (PCR+, HiSeqX) provided by DNAnexus
      • 2 replicates of HG001 (PCR+, NovaSeq) from BaseSpace public data.
    • Removal:
      • WES data
        (In v0.5.0, we trained our WGS model with WGS+WES data. This time we found that it didn’t help with WGS accuracy, so we removed them)
  2. Improved training data labels. See haplotype_labeler.py
  3. For direct inputs/outputs from cloud storage, we no longer support direct file I/O (like gs://deepvariant) due to bugs in htslib. Instead we recommend using gcsfuse to read/write data directly on GCS buckets. See “Inputs and Outputs” in DeepVariant user guide.