From 3eaae3afcada477857c29459fd5cf3ead3c2e078 Mon Sep 17 00:00:00 2001
From: Nicole Deflaux <deflaux@google.com>
Date: Thu, 15 Dec 2016 14:07:21 -0800
Subject: [PATCH] Add page for Platinum Genomes DeepVariant GRCh38 data.

Change-Id: Ibb766b99eeded27c991670cac1deb29334d4d85e
---
 .../discover_public_data/genomic_data_toc.rst |  1 +
 .../discover_public_data/platinum_genomes.rst |  2 +-
 .../platinum_genomes_deepvariant.rst          | 49 +++++++++++++++++++
 3 files changed, 51 insertions(+), 1 deletion(-)
 create mode 100644 docs/source/use_cases/discover_public_data/platinum_genomes_deepvariant.rst

diff --git a/docs/source/use_cases/discover_public_data/genomic_data_toc.rst b/docs/source/use_cases/discover_public_data/genomic_data_toc.rst
index d7bb2f0..658f5bb 100644
--- a/docs/source/use_cases/discover_public_data/genomic_data_toc.rst
+++ b/docs/source/use_cases/discover_public_data/genomic_data_toc.rst
@@ -22,6 +22,7 @@ __ RenderedVersion_
 
   1000_genomes
   platinum_genomes
+  platinum_genomes_deepvariant
   reference_genomes
   mssng_data
   isb_cgc_data
diff --git a/docs/source/use_cases/discover_public_data/platinum_genomes.rst b/docs/source/use_cases/discover_public_data/platinum_genomes.rst
index e5720af..d566b0c 100644
--- a/docs/source/use_cases/discover_public_data/platinum_genomes.rst
+++ b/docs/source/use_cases/discover_public_data/platinum_genomes.rst
@@ -17,7 +17,7 @@ __ RenderedVersion_
 
 .. comment: end: goto-read-the-docs
 
-This dataset comprises the 17 member CEPH pedigree 1463.  See http://www.illumina.com/platinumgenomes/ for full details.
+This dataset comprises the `6 member CEPH pedigree 1463 <http://www.ebi.ac.uk/ena/data/view/PRJEB3381>`_.  See http://www.illumina.com/platinumgenomes/ for full details.
 
 Google Cloud Platform data locations
 ------------------------------------
diff --git a/docs/source/use_cases/discover_public_data/platinum_genomes_deepvariant.rst b/docs/source/use_cases/discover_public_data/platinum_genomes_deepvariant.rst
new file mode 100644
index 0000000..85f8c81
--- /dev/null
+++ b/docs/source/use_cases/discover_public_data/platinum_genomes_deepvariant.rst
@@ -0,0 +1,49 @@
+Platinum Genomes DeepVariant
+============================
+
+.. comment: begin: goto-read-the-docs
+
+.. container:: visible-only-on-github
+
+   +-----------------------------------------------------------------------------------+
+   | **The properly rendered version of this document can be found at Read The Docs.** |
+   |                                                                                   |
+   | **If you are reading this on github, you should instead click** `here`__.         |
+   +-----------------------------------------------------------------------------------+
+
+.. _RenderedVersion: http://googlegenomics.readthedocs.org/en/latest/use_cases/discover_public_data/platinum_genomes.html
+
+__ RenderedVersion_
+
+.. comment: end: goto-read-the-docs
+
+This dataset comprises the `6 member CEPH pedigree 1463 <http://www.ebi.ac.uk/ena/data/view/PRJEB3381>`_ called using the DeepVariant toolchain and reference genome GRCh38.  See the `DeepVariant preprint <http://biorxiv.org/content/early/2016/12/14/092890>`_ for full details:
+
+|  `Creating a universal SNP and small indel variant caller with deep neural networks <http://biorxiv.org/content/early/2016/12/14/092890>`_
+|  Ryan Poplin, Dan Newburger, Jojo Dijamco, Nam Nguyen, Dion Loy, Sam Gross, Cory Y. McLean, Mark A. DePristo
+|  DOI: https://doi.org/10.1101/092890
+|
+
+Google Cloud Platform data locations
+------------------------------------
+
+* Google Cloud Storage folder `gs://genomics-public-data/platinum-genomes-deepvariant <https://console.cloud.google.com/storage/genomics-public-data/platinum-genomes-deepvariant/>`_
+* Google Genomics Dataset ID `14839180708999654392 <https://developers.google.com/apis-explorer/#p/genomics/v1/genomics.datasets.get?datasetId=14839180708999654392>`_
+
+  * `Variant Reference Bounds <https://developers.google.com/apis-explorer/#p/genomics/v1/genomics.variantsets.get?variantSetId=4775355778792783584>`_
+
+* Google BigQuery Dataset ID `genomics-public-data:platinum_genomes_deepvariant <https://bigquery.cloud.google.com/dataset/genomics-public-data:platinum_genomes_deepvariant>`_
+
+Provenance
+----------
+
+* The FASTQ files in `gs://genomics-public-data/platinum-genomes/fastq/ <https://console.cloud.google.com/storage/genomics-public-data/platinum-genomes/fastq/>`_ were run through the DeepVariant toolchain to produce the corresponding ``*.deepvariant.g.vcf`` and ``*.deepvariant.vcf`` files in `gs://genomics-public-data/platinum-genomes-deepvariant/vcf/ <https://console.cloud.google.com/storage/genomics-public-data/platinum-genomes-deepvariant/vcf/>`_.
+* These files were then imported to Google Genomics and the variants were exported to Google BigQuery as table `genomics-public-data:platinum_genomes_deepvariant.single_sample_genome_calls <https://bigquery.cloud.google.com/table/genomics-public-data:platinum_genomes_deepvariant.single_sample_genome_calls?tab=details>`_.
+* The data was then merged to produce variants-only `multisample-platinum-genomes-deepvariant.vcf <https://console.cloud.google.com/storage/genomics-public-data/platinum-genomes-deepvariant/multisample-vcf/>`_ and  table `genomics-public-data:platinum_genomes_deepvariant.multisample_variants <https://bigquery.cloud.google.com/table/genomics-public-data:platinum_genomes_deepvariant.multisample_variants?tab=details>`_.
+
+  * The merging logic:
+
+    * groups together only single- and multi-nucleotide polymorphisms with the same reference representation and alternate allele length that originate at the same chromosome and reference position
+    * merges all insertions at the same reference position, and
+    * splits complex variants into multiple records.
+  * Individual variants with GQ < 20 are hard-masked to no-calls, with the genotype likelihoods retained.