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Commits on Nov 21, 2019

• Report TF dependency fix.

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• Dockerfile fix for vcf_stats_report.

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• Add hyperlink to GLnexus GitHub.

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  cmclean

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• Merge branch 'r0.9' of github.com:google/deepvariant into r0.9

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Commits on Nov 13, 2019

• Update documentation.

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  pichuan

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• Update documentation.

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• Improve doc.

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• Improve doc.

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• Update doc.

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• Simplify workflow figure.

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• Update DeepVariantWGS and DeepVariantWES GLnexus configuration.

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• Use the docker from GLnexus directly. This allows the users to use newer GLnexus versions.

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• Update VCF stats report documentation with v0.9.0 case studies.

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  MariaNattestad

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• Update all r0.8 references to r0.9 in documentation

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• Crop image.

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• Update image.

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Commits on Nov 12, 2019

• Modify variant_utils.is_singleton to early return if variantion count is more

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• Automated g4 rollback of changelist 279419788

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• Update numbers and DeepVariant version for trio merging case study.

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• Case-study documentation updates for v0.9.0 release

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• Correct the description of the BAMs.

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Commits on Nov 11, 2019

• Update training tutorial.

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• add exclude_header to vcf.VcfWriter.

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Commits on Nov 9, 2019

• Automated g4 rollback of changelist 279156241

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Commits on Nov 8, 2019

• Modify TPUConfig

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• Update training tutorial. Simplify the best ckpt step.

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Commits on Nov 7, 2019

• Update case study scripts to version 0.9.0

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  sgoe1

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• Update for 0.9.0 release.

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Commits on Nov 6, 2019

• Update documentation.

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Commits on Nov 2, 2019

• Update the model version to 0.9.0.

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Commits on Nov 1, 2019

• Change the condition for filtering haplotypes in realigner. Now it is required that there is more than 0 coverage throughout the whole interval. As a result if this fix there will be some reads tha…

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  akolesnikov

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• Error fix in make_examples_test.variant_key() function.

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• Add glnexus_cli in the Docker image.

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• Use six to deal with different names in Python2 and 3, such as assertRaisesRegex and assertCountEqual.

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Commits on Oct 31, 2019

• Update deprecated Python test method aliases.

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  Genomics team in Google Brain

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