3e1960b35a07377b46bd83b8fd04387f182c6bd6
abenetpa
Fri May 15 10:52:51 2020 -0700
added three description pages for dbVar tracks refs #25424
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+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 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 lenth and type of variant. The
+variant overlap filter defines four bins within that range from which the user can choose.
+
+
+
+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 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
+
+