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/dbVarOther.html src/hg/makeDb/trackDb/human/dbVarOther.html
new file mode 100644
index 00000000000..297c1d5d911
--- /dev/null
+++ src/hg/makeDb/trackDb/human/dbVarOther.html
@@ -0,0 +1,130 @@
+Description
+
+This track displays structural variants (SVs) in
+dbVar that are not classified as
+common, somatic, or clinical. The track is defined by exclusion: it contains dbVar SVs minus
+
+
+- common variants (covered by the dbVar Common SV
+track)
+- variants with somatic origin (covered by the
+dbVar Somatic SV track)
+- clinical variants from ClinVar (covered by the
+ClinVar track)
+- variants of the types: short tandem repeat, interchromosomal translocation, intrachromosomal
+translocation
+- variants from a set of legacy or obsoleted dbVar studies (nstd45, nstd75, nstd90, estd59,
+estd199, estd214)
+- variants discovered using low-confidence methods (BAC aCGH, FISH, Karyotyping, MassSpec,
+Microsatellite genotyping, Multiple complete digestion, Not provided, ROMA, Southern, Western)
+
+
+
+NCBI sometimes refers to this category as presumed normal SVs in their hub documentation
+and source files. We use the term Other here to avoid implying that the variants are
+clinically normal — the track is purely a residual bucket of dbVar SVs that don't fit the
+other three composites.
+
+
+
+This track is updated with every monthly dbVar release.
+
+
+Subtracks
+
+The Other SVs are split into two subtracks:
+
+
+- dbVar Healthy SVs: SVs in dbVar with no reported phenotype.
+- dbVar Phenotype SVs: SVs in dbVar with a reported phenotype, excluding clinical
+and somatic variants.
+
+
+
+The Healthy subtrack is considerably larger than the Phenotype subtrack. Turning on
+Hide empty subtracks (default) limits the display to subtracks with data in the current
+viewing window.
+
+
+Display Conventions and Configuration
+
+Variants are colored by type, using the dbVar color scheme described in the
+dbVar Overview
+page:
+
+
+
+| Color |
+Variant Type(s) |
+
+
+ | deletion, delins, copy number loss |
|---|
+ | duplication, copy number gain, insertion |
|---|
+ | copy number variation |
|---|
+ | inversion |
|---|
+ | complex substitution |
|---|
+ | tandem duplication |
|---|
+ | sequence alteration |
|---|
+
+
+
+
+Mouseover on items shows gene(s) affected, size, variant type, dbVar study of origin,
+discovery method, phenotype (in the Phenotype subtrack), and population code (if available).
+
+
+
+Subtracks can be filtered by:
+
+
+- Variant Type
+- Variant Size (Under 10KB, 10KB to 100KB, 100KB to 1MB, Over 1MB)
+- Discovery Method (Curated, Merging, Multiple, Oligo aCGH, Optical mapping, SNP array,
+Sequencing, other)
+- Pathogenic Reciprocal Overlap (none, 10 to 25, 25 to 50, 50 to 75, 75 to 90, 90 to 100)
+— range of reciprocal overlap with pathogenic variants in nstd102
+- Population Code (AFR, AMR, EAS, EUR, OTH, SAS, mixed, multiple, none, unknown)
+
+
+Methods
+
+Per NCBI's dbVar processing pipeline, variant calls are extracted from the
+variant_calls.gvf files on the dbVar FTP site, reciprocally overlapped with the
+pathogenic clinical SV file using bedtools, filtered by the exclusion criteria described above,
+and converted to bigBed format. See the
+dbVar
+Overview for full methods.
+
+
+Data Access
+
+The raw data can be explored interactively with the
+Table Browser, or the
+Data Integrator. Due to the size of the Healthy subtrack (over
+5 million items), Table Browser queries on large regions may be slow — narrow by
+chromosome or region where possible.
+
+
+The data can also be downloaded from 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
+coordination and consultation.
+
+
+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
+