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Commits on Aug 6, 2021

• Update our DeepTrio case study GLnexus config to be DeepVariant_unfiltered.

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Commits on Jul 29, 2021

• Update version.

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• Update version.

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• Update metrics-deeptrio.md.

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Commits on Jul 27, 2021

• Update deeptrio training data.

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• Update the version links in the Python notebooks to be r1.2.

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• Add documentation for --include_med_dp.

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• Update metrics.md.

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Commits on Jul 26, 2021

• Update documents with latest version (1.2.0).

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• Update more *-case-study.md.

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Commits on Jul 25, 2021

• Update a few *-case-study.md files.

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• Update Quick Starts.

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Commits on Jul 19, 2021

• This is added in google#473 already. Submitting again to include in future releases as well.

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Commits on Jul 16, 2021

• Update the number of training examples based on the latest release candidates.

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Commits on Jul 12, 2021

• Update metrics-deeptrio.md with model from PacBio v1.2.0 release candidates, and with latest code. Keeping the WGS and WES models from v1.1.0 for now.

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Commits on Jul 9, 2021

• Update DeepVariant metrics.md with model from v1.2.0 release candidates, and with latest code.

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Commits on Jun 16, 2021

• Use bioconda to add bcftools and samtools to Dockerfile for DeepVariant and DeepTrio.

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Commits on Jun 8, 2021

• Update references of Ubuntu version to 20.04.

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Commits on Jun 4, 2021

• Update metrics-deeptrio.md with model from v1.1.0, and with latest code.

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Commits on Jun 2, 2021

• Update DeepVariant metrics.md with model from v1.1.0, and with latest code.

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Commits on Jun 1, 2021

• Add hybrid model example counts to documentation.

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Commits on May 26, 2021

• Resubmit a previous change:

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Commits on May 24, 2021

• Update DeepVariant metrics.md with model from v1.1.0, and with latest code.

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Commits on May 18, 2021

• Automated g4 rollback of changelist 374425378

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• * Update CPU use to Ubuntu20.04

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Commits on May 5, 2021

• Update FAQ with AD/DP calc details.

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Commits on Apr 7, 2021

• Update shuffle_tfrecords_beam.py to output number of examples of each class.

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Commits on Mar 30, 2021

• Add FAQ.

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Commits on Mar 25, 2021

• Update runtime-by-region documentation.

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Commits on Mar 22, 2021

• Update metrics-deeptrio.md with Docker version 1.1.0, but with jmcdani20/hap.py:v0.3.12 hap.py and truth version v4.2.1.

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Commits on Mar 17, 2021

• Update metrics.md with Docker version 1.1.0, but with jmcdani20/hap.py:v0.3.12 hap.py and truth version v4.2.1.

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Commits on Mar 15, 2021

• Update truth version to v4.2.1.

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• Add --pass-only to all hap.py evaluation for DeepVariant and DeepTrio.

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• Re-run and update the documentation with the new hap.py version and new truth to make sure results are updated.

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Commits on Mar 10, 2021

• Fix typo for GLnexus.

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