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/dbVarCurated.html src/hg/makeDb/trackDb/human/dbVarCurated.html index c34af448450..a90e666c4fb 100644 --- src/hg/makeDb/trackDb/human/dbVarCurated.html +++ src/hg/makeDb/trackDb/human/dbVarCurated.html @@ -1,99 +1,130 @@

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: +This super-track groups structural variant (SV) tracks from +dbVar, NCBI's archive of human +genomic structural variation. The data are mirrored from the +NCBI dbVar track +hub.

-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.

+There are four track collections in this super-track: +

+ +

-DECIPHER Common CNVs -(nstd183): -Consensus set of common population CNVs selected from high-resolution controls sets where frequency -information is available. +Clinical structural variants from dbVar study nstd102 are not duplicated here; they are available +in our dedicated ClinVar track (subtrack +ClinVar CNVs), which pulls from the same underlying ClinVar XML release.

+

Source Studies in nstd186 (Common SV)

-There are two tracks in this collection: +nstd186 is a +curated collection of SVs from studies with at least 100 samples and allele frequency >= 0.01 +in at least one population. It aggregates data from six source studies: +

+ +

+Variants must be of a qualifying structural variant type (deletions, duplications, insertions, +copy number variants, and mobile element variants). For the latest statistics and version +history, see the +nstd186 summary +page at NCBI.

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. +These tracks are composite tracks that contain multiple subtracks. Each subtrack has its own +display controls, as described here. Items are +colored by variant type using the dbVar color scheme +(dbVar Overview): +

+ + + + + + + + + + +
ColorVariant Type(s)
deletion, copy number loss
duplication, copy number gain, insertion
copy number variation
+

+Some composites display additional colors for less common variant types. Refer to each composite +track's description page for the full legend.

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, where additional subtracks (e.g., population-exclusive variants, ClinVar SVs) are +available. 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.

+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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