b85c12cf9af0ee1a954b8cced961bcbd909b7979 lrnassar Wed Apr 29 12:04:36 2026 -0700 Expand dbVar tracks to expose all six nstd186 source studies and add new Somatic and Other composites. refs #37406 Restructure the dbVar supertrack: - Renamed from "dbVar Common Struct Var" to "dbVar Struct Var". - dbVar Common SV: added subtracks for Lee, Abel, and Byrska-Bishop (the three nstd186 source studies that were missing from our Curated Common track), and for the American/East Asian/South Asian/Other populations. - dbVar Conflict SV: description page refreshed; subtrack longLabel clarified. - dbVar Somatic SV (new): single subtrack pulling somatic_sv.bb from the dbVar hub. Default hidden. - dbVar Other SV (new): residual bucket for dbVar SVs not classified as common, somatic, or clinical, split into Healthy and Phenotype subtracks. Default hidden. NCBI sometimes calls this "presumed normal"; the description page notes the equivalence. mergeSpannedItems on for the dense subtracks (normal_healthy ~5.6M items, normal_phenotype ~410K, somatic_sv ~67K). - ClinVar SVs are not duplicated; description pages cross-link to the existing ClinVar track instead. Description pages: rewrite dbVarCommon.html and dbVarCurated.html, refresh dbVarConflict.html, add dbVarSomatic.html and dbVarOther.html. Retire the unused dbVar_common.html. Methods links now point at NCBI's dbVar Overview rather than the FTP directory listing. searchTable termRegex widened to ^[den]ssv[0-9]+ so dssv* accessions in normal_healthy resolve. Otto: stage downloads to release/\${db}.new/, validate per file (size floor and 10% itemCount delta vs the current live copy), then atomically swap via directory rename with a one-cycle .prev rollback. On validation failure, leave .new/ in place for human inspection and exit non-zero so the wrapper emails. On no-op runs the wrapper now stays silent. checkNstd175.sh's "update done" message moved inside the update branch so silence is honoured. New-file detection (via a knownFiles.txt manifest) emails when NCBI adds a file we don't yet expose. knownFiles.txt itself lives only at the deployment path under /hive/data/outside/otto/dbVar/, not in the tree. diff --git src/hg/makeDb/trackDb/human/dbVarCommon.html src/hg/makeDb/trackDb/human/dbVarCommon.html index 015acbff1e5..cce6a323ed3 100644 --- src/hg/makeDb/trackDb/human/dbVarCommon.html +++ src/hg/makeDb/trackDb/human/dbVarCommon.html @@ -1,110 +1,158 @@

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 track displays common structural variants (SVs) from +nstd186 +(NCBI Curated Common Structural Variants), divided into subtracks by source study and by +population.

-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). +nstd186 is a curated collection of structural variants in +dbVar from studies with at least +100 samples, that include allele frequency data, and that have an allele frequency of >=0.01 +in at least one population. It includes copy number gains and losses, copy number variations, +duplications, deletions, insertions, and mobile element variants (ALU, LINE1, SVA, HERV).

-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. +The dataset aggregates variants from six source studies:

+

-For more information on the number of variant calls and latest statistics for nstd186 see -Summary of nstd186 -(NCBI Curated Common Structural Variants). +For the latest nstd186 variant call counts and version history, see the +nstd186 +summary page at NCBI.

+

Subtracks

+

-There are six subtracks in this track set: +Per-source-study subtracks (variants from nstd186 attributed to one of the six component +studies):

+

+Per-population subtracks (variants with AF >= 0.01 aggregated across nstd186 source +studies for each super-population): +

+ +

+The NCBI dbVar +Track Hub additionally provides population-only variants (variants common in one +population but not in any other): African only, American only, East Asian only, European only, +and South Asian only. These are not loaded as native Genome Browser tracks; connect to the hub to +view them.

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. + +

+Items in all subtracks follow the same conventions. Variants are colored by type, using the dbVar +color scheme described in the +dbVar Overview +page:

+ + + + + + + + + + +
ColorVariant Type(s)
copy number loss, deletion (including mobile element deletions)
copy number gain, duplication, insertion (including mobile element insertions)
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. +Mouseover on items shows genes affected, size, variant type, allele count (AC), allele +number (AN), allele frequency (AF), and population (in per-population subtracks). +

+ +

+Subtracks can be filtered by: +

+ + +

+The Hide empty subtracks option on the track configuration page hides subtracks that have +no data in the current viewing window. This is enabled by default and can be toggled off.

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, 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 -. +

+The data can also be found directly at the +dbVar +nstd186 data access page, or in the +dbVar +Track Hub. 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 +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 +PMID: 23193291; +PMC: PMC3531204

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