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/dbVarCurated.html src/hg/makeDb/trackDb/human/dbVarCurated.html new file mode 100644 index 0000000..232f461 --- /dev/null +++ src/hg/makeDb/trackDb/human/dbVarCurated.html @@ -0,0 +1,85 @@ +

Description

+

+The tracks listed here contain data from the + +nstd186 (NCBI Curated Common Structural Variants) study. This is a collection of structural +variants (SV) originally submitted to dbVar which are part of a study with at least 100 samples and +have an allele frequency of >=0.01 in at least one population. The complete dataset is imported +from these common-population studies: +

+ +

+gnomAD Structural Variants +(nstd166): + Catalog of SVs detected from the sequencing of the complete genome of 10,847 unrelated +individuals from the GnomAD v2.1 release.

+

+1000 Genomes Consortium Phase 3 Integrated SV +(estd219): + Structural variants of the 1000 Genomes project Phase 3 as reported in a separate article +specifically dedicated to the analysis of SVs. Many of these data are identical to those reported +in the estd214 study.

+

+DECIPHER Common CNVs +(nstd183): +Consensus set of common population CNVs selected from high-resolution controls sets where frequency +information is available. +

+ +

+There are two tracks in this collection: +

+

+ +

Display Conventions

+

+These tracks are multi-view composite tracks that contain multiple data types (views). Each view +within a track has separate display controls, as described +here. Some dbVar tracks +contain multiple subtracks, corresponding to subsets of data. If a track contains many subtracks, +only some subtracks will be displayed by default. The user can select which subtracks are displayed +via the display controls on the track details page. +

+ +

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 +

+