dc28e7eaba410716bba6a5f86c78a11b9e817a61
dschmelt
Mon Oct 5 15:04:15 2020 -0700
Small link fixes for dbVar refs #25423
diff --git src/hg/makeDb/trackDb/human/dbVarConflict.html src/hg/makeDb/trackDb/human/dbVarConflict.html
index d2c005d..d509497 100644
--- src/hg/makeDb/trackDb/human/dbVarConflict.html
+++ src/hg/makeDb/trackDb/human/dbVarConflict.html
@@ -1,71 +1,82 @@
Description
The track NCBI dbVar Curated Common SVs: Conflicts with Pathogenic highlights loci where
common copy number variants from
nstd186 (NCBI Curated
Common Structural Variants) overlap with structural Variants with clinical assertions,
submitted to ClinVar by external labs (Clinical Structural
Variants - nstd102).
Overlap in the track refers to reciprocal overlap between variants in the common
(NCBI Curated Common Structural Variants) versus clinical (ClinVar Long Variants)
tracks. Reciprocal overlap values can be anywhere from 10% to 100%.
For more information on the number of variant calls and latest statistics for nstd186 see
Summary of nstd186
(NCBI Curated Common Structural Variants).
Display Conventions and Configuration
Items in all subtracks follow the same conventions: items are colored by variant type, and are
based on the dbVar colors described in the
dbVar Overview page.
Red for copy number loss or deletion,
blue for copy number gain or duplication, and
violet for copy number variation.
Mouseover on items indicates genes affected, size, variant type, and allele frequencies (AF).
All tracks can be filtered according to the variant length, variant type and
variant overlap. This last filter defines four bins within that range from which the
user can choose.
Data Access
The raw data can be explored interactively with the
-Table Browser, or the
-Data Integrator. For automated analysis,
+Table Browser, or the
+Data Integrator. For automated analysis,
the data may be queried from our
-REST API. The data can also be found
-directly from the dbVar nstd186 data access, as
-well as in the dbVar Track Hub, where additional subtracks are included. For questions about dbVar track
-data, please contact dbvar@ncbi.nlm.nih.gov.
+REST API.
+
+
+The data can also be found directly from the dbVar
+nstd186 data access, as well as in the
+
+dbVar Track Hub, where additional subtracks are included. For questions about
+dbVar track data, please contact
+dbvar@ncbi.
+nlm.
+nih.
+gov.
+
-Credits
Thanks to the dbVAR team at NCBI, especially John Lopez and Timothy Hefferon for technical
coordination and consultation, and to Christopher Lee, Anna Benet-Pages, and Daniel Schmelter of
the Genome Browser team for engineering the track display.
References
Lappalainen I, Lopez J, Skipper L, Hefferon T, Spalding JD, Garner J, Chen C, Maguire M, Corbett M,
Zhou G et al.
DbVar and DGVa: public archives for genomic structural variation.
Nucleic Acids Res. 2013 Jan;41(Database issue):D936-41.
PMID: 23193291; PMC: PMC3531204