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Htslib updated to v1.9, fixing an outstanding CRAM issue.
Fix for the issue of non-deterministic output caused by changing number of shards in the make_example process.
Upgrade to TensorFlow v1.12.
Speed improvements in make_examples via the use of a flat_hash_map.
Speed improvements in call_variants.
The genotypes of low-quality (GQ < 20) homozygous reference calls are set to ./. instead of 0/0. The threshold is configurable via --cnn_homref_call_min_gq flag in postprocess_variants.py. This improves downstream cohort merging performance based on our internal investigation in a "Improved non-human variant calling using species-specific DeepVariant models" blog.
Google Cloud Runner:
Localize BED region files (given via --region flag), fixing an outstanding issue.
Make worker logs available in case of a failure inside DeepVariant.
