40710f848501eb48692babdc889a513f3dcda7ef abenetpa Fri Sep 25 09:01:51 2020 -0700 improved color code descriptions refs #25424 diff --git src/hg/makeDb/trackDb/human/dbVarConflict.html src/hg/makeDb/trackDb/human/dbVarConflict.html index 11e5a5c..2cd6167 100644 --- src/hg/makeDb/trackDb/human/dbVarConflict.html +++ src/hg/makeDb/trackDb/human/dbVarConflict.html @@ -9,53 +9,59 @@

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). + +

+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.

-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. +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, the data may be queried from our REST API.

The data can also be found directly from the dbVar nstd186 -data access. +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.