3e1960b35a07377b46bd83b8fd04387f182c6bd6
abenetpa
Fri May 15 10:52:51 2020 -0700
added three description pages for dbVar tracks refs #25424
diff --git src/hg/makeDb/trackDb/human/dbVarCommon.html src/hg/makeDb/trackDb/human/dbVarCommon.html
new file mode 100644
index 0000000..d2f88c4
--- /dev/null
+++ src/hg/makeDb/trackDb/human/dbVarCommon.html
@@ -0,0 +1,92 @@
+ Description
+
+
+This track displays common copy number genomic variations from nstd186 (NCBI Curated Common
+Structural Variants), divided into subtracks according to population and source of original
+submission.
+
+
+
+This curated dataset of all structural variants in dbVar includes variants from gnomAD, 1000
+Genomes Phase 3, and DECIPHER (dbVar studies
+nstd166,
+estd219, and
+nstd183, respectively).
+
+
+
+It only includes copy number gain, copy number loss, copy number variation, duplications, and
+deletions (including mobile element deletions), that are part of a study with at least 100 samples,
+include allele frequency data, and have an allele frequency of >=0.01 in at least one population.
+
+
+
+For more information on the number of variant calls and latest statistics for nstd186 see
+Summary of nstd186
+(NCBI Curated Common Structural Variants).
+
+
+
+There are six subtracks in this track set:
+
+
+
+
+- NCBI Curated Common SVs: African -
+Variants with AF >= 0.01 for
+African Population.
+- NCBI Curated Common SVs: European -
+Variants with AF >= 0.01 for
+European Population.
+- NCBI Curated Common SVs: all populations -
+Variants with AF >= 0.01 for
+Global Population.
+- NCBI Curated Common SVs: all populations from gnomAD -
+Variants with AF >= 0.01 from
+gnomAD Structural Variants.
+- NCBI Curated Common SVs: all populations from 1000 Genomes -
+Variants with AF >= 0.01 from
+1000 Genomes Consortium Phase 3 Integrated SV.
+- NCBI Curated Common SVs: all populations from DECIPHER -
+Variants with AF >= 0.01 from
+DECIPHER Consensus CNVs.
+
+
+
+Display Conventions and Configuration
+Items in all subtracks follow the same conventions: items are shaded according to variant type.
+Red for copy number loss or deletion,
+blue for copy number gain or duplication and
+violet for copy number variation. Mouseover on items indicates
+Allele Frequencies (AF). All tracks can be filtered according to the Variant Size and Variant Type.
+
+Data Acces
+The raw data can be explored interactively with the
+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.
+For questions about dbVar track data, please contact dbvar@ncbi.nlm.nih.gov.
+
+
+Credits
+
+Thanks to the dbVAR team at NCBI, especially Timothy Hefferon for technical coordination and
+consultation, and to Christopher Lee, Anna Benet-Pages, and Maximilian Haeussler of the Genom
+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
+
+
+