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updated stats in data page.
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@newgene
newgene committed Jul 28, 2015
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Expand Up @@ -8,7 +8,7 @@ Variant annotation data
Data sources
------------

We currently obtain variant annotation data from several data resources and
We currently obtain variant annotation data from several data resources and
keep them up-to-date, so that you don't have to do it:

.. _dbNSFP: https://sites.google.com/site/jpopgen/dbNSFP
Expand All @@ -21,40 +21,46 @@ keep them up-to-date, so that you don't have to do it:
.. _COSMIC: http://cancer.sanger.ac.uk/cancergenome/projects/cosmic/
.. _DOCM: http://docm.genome.wustl.edu/
.. _SNPedia: http://www.snpedia.com
.. _EMVClass: http://geneticslab.emory.edu/emvclass/emvclass.php
.. _EMVClass: http://geneticslab.emory.edu/emvclass/emvclass.php
.. _Scripps Wellderly: http://www.stsiweb.org/wellderly/
.. _EXAC: http://exac.broadinstitute.org/
.. _GRASP: http://iapps.nhlbi.nih.gov/GRASP

Total variants loaded: **286,219,908**
Total variants loaded: **288,654,586**

+-------------------------------+---------------+---------------------------+----------------------------+
| Source | version | # of variants | key name* |
+===============================+===============+===========================+============================+
| `dbNSFP`_ |v2.9 | 78,045,379 | dbnsfp |
| `dbNSFP`_ |v3.0b2 | 82,027,652 | dbnsfp |
+-------------------------------+---------------+---------------------------+----------------------------+
| `dbSNP`_ |v142 | 110,234,210 |dbsnp |
| `dbSNP`_ |v142 | 110,234,202 |dbsnp |
+-------------------------------+---------------+---------------------------+----------------------------+
| `ClinVar`_ |20150323 |85,789 |clinvar |
| `ClinVar`_ |20150323 |85,775 |clinvar |
+-------------------------------+---------------+---------------------------+----------------------------+
| `EVS`_ | v2 | 1,977,300 | evs |
| `EVS`_ | v2 | 1,977,296 | evs |
+-------------------------------+---------------+---------------------------+----------------------------+
| `CADD`_ | v1.2 | 163,690,986 | cadd |
| `CADD`_ | v1.2 | 163,690,938 | cadd |
+-------------------------------+---------------+---------------------------+----------------------------+
| `MutDB`_ | \- | 420,221 |mutdb |
| `MutDB`_ | \- | 420,220 |mutdb |
+-------------------------------+---------------+---------------------------+----------------------------+
| `GWAS Catalog`_ |from UCSC |15,243 |gwassnps |
+-------------------------------+---------------+---------------------------+----------------------------+
| `COSMIC`_ |v68 from UCSC |1,024,498 |cosmic |
| `COSMIC`_ |v68 from UCSC |1,024,496 |cosmic |
+-------------------------------+---------------+---------------------------+----------------------------+
| `DOCM`_ | \- | 1,119 | docm |
+-------------------------------+---------------+---------------------------+----------------------------+
| `SNPedia`_ | \- | 5,907 | snpedia |
+-------------------------------+---------------+---------------------------+----------------------------+
| `EMVClass`_ | \- | 12,066 |emv |
+-------------------------------+---------------+---------------------------+----------------------------+
| `Scripps Wellderly`_ | \- |21,240,519 | wellderly |
| `Scripps Wellderly`_ | \- |21,240,518 | wellderly |
+-------------------------------+---------------+---------------------------+----------------------------+
| `EXAC`_ | v0.3 |10,195,861 | exac |
+-------------------------------+---------------+---------------------------+----------------------------+
| `GRASP`_ | v2.0.0.0 |2,212,148 | grasp |
+-------------------------------+---------------+---------------------------+----------------------------+

\* key name: this is the key for the specific annotation data in a variant object.
\* key name: this is the key for the specific annotation data in a variant object.

The most updated information can be accessed `here <http://myvariant.info/v1/metadata>`_.

Expand All @@ -66,11 +72,11 @@ The most updated information can be accessed `here <http://myvariant.info/v1/met
Variant object
---------------

Variant annotation data are both stored and returned as a variant object, which
Variant annotation data are both stored and returned as a variant object, which
is essentially a collection of fields (attributes) and their values:

.. code-block :: json
{
"_id": "chr1:g.35367G>A",
"_version": 2,
Expand All @@ -87,7 +93,7 @@ is essentially a collection of fields (attributes) and their values:
"gene_id": "ENSG00000237613",
},
"ref": "G",
"type": "SNV"
"type": "SNV"
},
"dbnsfp": {
"aa": {
Expand All @@ -113,7 +119,7 @@ is essentially a collection of fields (attributes) and their values:
}
}
The example above omits many of the available fields. For a full example,
The example above omits many of the available fields. For a full example,
check out `this example variant <http://myvariant.info/v1/variant/chr1:g.35367G%3EA>`_, or try the `interactive API page <http://myvariant.info/v1/api>`_.

.. _available_fields:
Expand Down Expand Up @@ -157,4 +163,4 @@ or as inputs to the fields parameter, e.g.
</tbody>
</table>

<div id="spacer" style="height:300px"></div>
<div id="spacer" style="height:300px"></div>

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