acca3deffc05c4d8d11590a1cf3d893763254712
angie
Thu Oct 31 13:43:05 2019 -0700
dbSnp153: Adding new ucscNotes suggested by Ana Benet: clinvar{Benign,Conflicting,Pathogenic}, rareAll, rareSome. refs #23283
diff --git src/hg/makeDb/trackDb/human/dbSnp153Composite.html src/hg/makeDb/trackDb/human/dbSnp153Composite.html
index e34d5b8..d74342c 100644
--- src/hg/makeDb/trackDb/human/dbSnp153Composite.html
+++ src/hg/makeDb/trackDb/human/dbSnp153Composite.html
@@ -177,30 +177,48 @@
UCSC annotates some properties of interest.
These are noted on the item details page,
and may be useful to include or exclude affected variants.
Some are purely informational:
</p>
<table class="descTbl">
<tr><th>keyword in data file (dbSnp152.bb)</th>
<th># in hg19</th><th># in hg38</th><th>description</th></tr>
<tr>
<td>clinvar</td>
<td class="number">454656</td>
<td class="number">453954</td>
<td>Variant is in ClinVar.</td>
</tr>
<tr>
+ <td>clinvarBenign</td>
+ <td class="number">143844</td>
+ <td class="number">143696</td>
+ <td>Variant is in ClinVar with clinical significance of benign and/or likely benign.</td>
+ </tr>
+ <tr>
+ <td>clinvarConflicting</td>
+ <td class="number">7932</td>
+ <td class="number">7950</td>
+ <td>Variant is in ClinVar with reports of both benign and pathogenic significance.</td>
+ </tr>
+ <tr>
+ <td>clinvarPathogenic</td>
+ <td class="number">96242</td>
+ <td class="number">95262</td>
+ <td>Variant is in ClinVar with clinical significance of pathogenic and/or likely pathogenic.</td>
+ </tr>
+ <tr>
<td>commonAll</td>
<td class="number">12178426</td>
<td class="number">12430253</td>
<td>Variant is "common", i.e. has a Minor Allele Frequency of at least 1% in all
projects reporting frequencies.</td>
</tr>
<tr>
<td>commonSome</td>
<td class="number">20534330</td>
<td class="number">20893174</td>
<td>Variant is "common", i.e. has a Minor Allele Frequency of at least 1% in some, but not all,
projects reporting frequencies.</td>
</tr>
<tr>
<td>diffMajor</td>
@@ -209,30 +227,45 @@
<td>Different frequency sources have different major alleles.</td>
</tr>
<tr>
<td>overlapDiffClass</td>
<td class="number">106940656</td>
<td class="number">109838613</td>
<td>This variant overlaps another variant with a different type/class.</td>
</tr>
<tr>
<td>overlapSameClass</td>
<td class="number">16890303</td>
<td class="number">17228657</td>
<td>This variant overlaps another with the same type/class but different start/end.</td>
</tr>
<tr>
+ <td>rareAll</td>
+ <td class="number">662571654</td>
+ <td class="number">681626796</td>
+ <td>Variant is "rare", i.e. has a Minor Allele Frequency of less than 1%
+ in all projects reporting frequencies, or has been reported without frequency data.</td>
+ </tr>
+ <tr>
+ <td>rareSome</td>
+ <td class="number">670927558</td>
+ <td class="number">690089717</td>
+ <td>Variant is "rare", i.e. has a Minor Allele Frequency of less than 1%
+ in some, but not all, projects reporting frequencies, or has been reported without
+ frequency data.</td>
+ </tr>
+ <tr>
<td>revStrand</td>
<td class="number">3813390</td>
<td class="number">4512600</td>
<td>The orientation of the currently viewed reference genome sequence is different from
the orientation of dbSNP's preferred top-level assembly sequence;
alleles are presented on the forward strand of the currently viewed reference sequence.</td>
</tr>
</table>
<p>
while others may indicate that the reference genome contains a rare variant or sequencing issue:
</p>
<table class="descTbl">
<tr><th>keyword in data file (dbSnp152.bb)</th>
<th># in hg19</th><th># in hg38</th><th>description</th></tr>
<tr>
@@ -340,33 +373,32 @@
<a href="ftp://ftp.ncbi.nlm.nih.gov/snp/archive/b153/JSON/"
target=_blank>ftp://ftp.ncbi.nlm.nih.gov/snp/archive/b153/JSON/</a>,
extracted a subset of the information about each variant, and collated
it into a bigBed file using the
<a href="https://genome-source.gi.ucsc.edu/gitlist/kent.git/blob/master/src/hg/lib/bigDbSnp.as"
target=_blank>bigDbSnp.as</a> schema with the information
necessary for filtering and displaying the variants,
as well as a separate file containing more detailed information to be
displayed on each variant's details page
(<a href="https://genome-source.gi.ucsc.edu/gitlist/kent.git/blob/master/src/hg/lib/dbSnpDetails.as"
target=_blank>dbSnpDetails.as</a> schema).
<h2>Data Access</h2>
<p>
The raw data underlying the UCSC Genome Browser track can be explored interactively with the
-<a href="../../cgi-bin/hgTables" target=_blank>Table Browser</a>,
-<a href="../../cgi-bin/hgIntegrator" target=_blank>Data Integrator</a>,
-or <a href="../../cgi-bin/hgVai" target=_blank>Variant Annotation Integrator</a>.
+<a href="../../cgi-bin/hgTables" target=_blank>Table Browser</a> or
+<a href="../../cgi-bin/hgIntegrator" target=_blank>Data Integrator</a>.
For automated analysis, the track data files can be downloaded from the downloads server for
<a href="http://hgdownload.soe.ucsc.edu/gbdb/hg38/snp/" target=_blank>hg38</a> and
<a href="http://hgdownload.soe.ucsc.edu/gbdb/hg19/snp/" target=_blank>hg19</a>
(dbSnp153.bb); the detailed variant properties can be downloaded from
<a href="http://hgdownload.soe.ucsc.edu/gbdb/hgFixed/dbSnp/" target=_blank>hgFixed</a>
(dbSnp153Details.tab.gz).
</p><p>
Please refer to our
<A HREF="https://groups.google.com/a/soe.ucsc.edu/forum/?hl=en&fromgroups#!search/download+snps"
target=_blank>mailing list archives</a>
for questions and example queries, or our
<a HREF="../FAQ/FAQdownloads.html#download36" target=_blank>Data Access FAQ</a>
for more information.
</p>