DeepVariant 0.6.0

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.