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/dbVarSomatic.html src/hg/makeDb/trackDb/human/dbVarSomatic.html
new file mode 100644
index 00000000000..b98fa8a15e4
--- /dev/null
+++ src/hg/makeDb/trackDb/human/dbVarSomatic.html
@@ -0,0 +1,118 @@
+Description
+
+This track displays structural variants (SVs) in
+dbVar with somatic origin,
+aggregated from six dbVar studies.
+
+
+
+Source studies:
+
+
+- COSMIC
+(estd192) —
+the Catalogue Of Somatic Mutations In Cancer.
+- Clinical Structural Variants
+(nstd102) —
+somatic subset of ClinVar SVs.
+- Ghazali et al. 2021
+(nstd202).
+- Helman et al. 2014
+(nstd94).
+- Walter et al. 2009
+(nstd11).
+- Wills et al. 2016
+(nstd125).
+
+
+
+This track is updated with every monthly dbVar release.
+
+
+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, copy number loss |
|---|
+ | duplication, copy number gain, insertion, mobile element insertion |
|---|
+ | inversion |
|---|
+ | complex substitution |
|---|
+ | tandem duplication |
|---|
+
+
+
+
+Mouseover on items shows gene(s) affected, size, variant type, source dbVar study, and
+discovery method.
+
+
+
+The track can be filtered by:
+
+
+- Variant Type
+- Variant Size (Under 10KB, 10KB to 100KB, 100KB to 1MB, Over 1MB)
+- Discovery Method (Curated, Multiple, SNP array, Sequencing)
+- 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
+
+
+Methods
+
+Per NCBI's dbVar processing pipeline, somatic variant calls are extracted from the
+variant_calls.somatic.gvf files on the dbVar FTP site, reciprocally overlapped
+with the pathogenic clinical SV file using bedtools, 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. For automated analysis,
+the data may be queried from our
+REST API.
+
+
+The data can also be downloaded from the
+dbVar Track Hub,
+or via the dbVar FTP in VCF, GVF, or tab-delimited formats. 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
+
+
+Tate JG, Bamford S, Jubb HC, Sondka Z, Beare DM, Bindal N, Boutselakis H, Cole CG, Creatore C,
+Dawson E et al.
+
+COSMIC: the Catalogue Of Somatic Mutations In Cancer.
+Nucleic Acids Res. 2019 Jan 8;47(D1):D941-D947.
+PMID: 30371878;
+PMC: PMC6323903
+