dc28e7eaba410716bba6a5f86c78a11b9e817a61 dschmelt Mon Oct 5 15:04:15 2020 -0700 Small link fixes for dbVar refs #25423 diff --git src/hg/makeDb/trackDb/human/dbVarCommon.html src/hg/makeDb/trackDb/human/dbVarCommon.html index e22e470..015acbf 100644 --- src/hg/makeDb/trackDb/human/dbVarCommon.html +++ src/hg/makeDb/trackDb/human/dbVarCommon.html @@ -1,102 +1,110 @@

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 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 Size and Variant Type.

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