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Data in Google Genomics
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`Google Genomics <https://cloud.google.com/genomics/>`_ was a database-backed technology that allowed users to query 
reads and variants using the 
`GA4GH API <https://media.readthedocs.org/pdf/ga4gh-schemas/latest/ga4gh-schemas.pdf>`_.

On December 7th, 2017 Google announced that the "reads API" has been replaced by the `htsget protocol <http://samtools.github.io/hts-specs/htsget.html>`_ , and the "variants API" has been replaced by htsget and the new open-source `"Variant Transforms" <https://github.com/googlegenomics/gcp-variant-transforms>`_ a tool for uploading variant data directly into BigQuery.

In 2017, the GA4GH team introduced the **htsget protocol** to allow users to download read data for subsections of the genome in which they are interested. This is a richer and more flexible approach to working with reads data. It allows you to keep your genomics data in a common BAM file format on Google Cloud Storage and work with it efficiently from your computation pipelines, using standard bioinformatics tools. Google has already launched their own `open source implementation <https://github.com/googlegenomics/htsget>`_ of this protocol, which you can use to access your reads data. Many popular tools such as samtools and htslib have been updated by the community to support htsget. Documentation is provided `here <https://github.com/googlegenomics/htsget/blob/master/README.md>`_. 

After analyzing usage of the Variants API, Google found that users primarily used it to import variant data and then export it to BigQuery. To save time and effort, Google created **Variant Transforms**, an open source tool for directly importing VCF data into BigQuery. Variant Transforms and its documentation is published `here <https://github.com/googlegenomics/gcp-variant-transforms>`_. Variant Transforms is more scalable than the legacy Variants API, and it has a robust roadmap with a dedicated Google team.


Because of the new APIs described above, ISB-CGC has removed the CCLE DNA-Seq and RNA-Seq data previously hosted in Google Genomics.  Please don't hesitate to reach out to us at feedback@isb-cgc.org if there are issues you would like to discuss or get help with.  Google also has a set of resources to follow `on GitHub <https://github.com/googlegenomics>`_.