cea47d47e8b2d70f5655d5947669e15d59c079d6 max Thu Apr 30 02:59:15 2026 -0700 committing dbVar nr track, keeping it only on dev, may be useful one day when looking at a CNV and for comparing against the new normal dbVar track diff --git src/hg/makeDb/trackDb/human/trackDb.dbVar.ra src/hg/makeDb/trackDb/human/trackDb.dbVar.ra index c423fbe9595..8dded823d07 100644 --- src/hg/makeDb/trackDb/human/trackDb.dbVar.ra +++ src/hg/makeDb/trackDb/human/trackDb.dbVar.ra @@ -1,139 +1,179 @@ track dbVarSv superTrack on group varRep html dbVarCurated shortLabel dbVar Common Struct Var longLabel NCBI Curated Common Structural Variants from dbVar track dbVar_common superTrack dbVarSv pack group varRep compositeTrack on visibility pack itemRgb on type bigBed 9 + . html dbVarCommon shortLabel dbVar Common SV longLabel NCBI dbVar Curated Common Structural Variants mouseOverField label searchIndex name filterLabel.type Variant Type filterValues.type alu deletion,copy number gain,copy number loss,copy number variation,deletion,duplication,herv deletion,line1 deletion,sva deletion filterLabel.length Variant Size filterValues.length Under 10KB,10KB to 100KB,100KB to 1MB,Over 1MB track dbVar_common_gnomad parent dbVar_common on shortLabel dbVar Curated gnomAD SVs longLabel NCBI dbVar Curated Common SVs: all populations from gnomAD bigDataUrl /gbdb/$D/bbi/dbVar/common_gnomad.bb type bigBed 9 + . url https://www.ncbi.nlm.nih.gov/dbvar/variants/$$ urlLabel NCBI Variant Page: track dbVar_common_1000g parent dbVar_common on shortLabel dbVar Curated 1000 Genomes SVs longLabel NCBI dbVar Curated Common SVs: all populations from 1000 Genomes bigDataUrl /gbdb/$D/bbi/dbVar/common_1000g.bb type bigBed 9 + . url https://www.ncbi.nlm.nih.gov/dbvar/variants/$$ urlLabel NCBI Variant Page: track dbVar_common_decipher parent dbVar_common on shortLabel dbVar Curated DECIPHER SVs longLabel NCBI dbVar Curated Common SVs: all populations from DECIPHER bigDataUrl /gbdb/$D/bbi/dbVar/common_decipher.bb type bigBed 9 + . url https://www.ncbi.nlm.nih.gov/dbvar/variants/$$ urlLabel NCBI Variant Page: track dbVar_common_african parent dbVar_common on shortLabel dbVar Curated African SVs longLabel NCBI dbVar Curated Common SVs: African bigDataUrl /gbdb/$D/bbi/dbVar/common_african.bb type bigBed 9 + . url https://www.ncbi.nlm.nih.gov/dbvar/variants/$$ urlLabel NCBI Variant Page: track dbVar_common_european parent dbVar_common on shortLabel dbVar Curated European SVs longLabel NCBI dbVar Curated Common SVs: European bigDataUrl /gbdb/$D/bbi/dbVar/common_european.bb type bigBed 9 + . url https://www.ncbi.nlm.nih.gov/dbvar/variants/$$ urlLabel NCBI Variant Page: track dbVar_common_global parent dbVar_common on shortLabel dbVar Curated All Populations longLabel NCBI dbVar Curated Common SVs: all populations bigDataUrl /gbdb/$D/bbi/dbVar/common_global.bb type bigBed 9 + . url https://www.ncbi.nlm.nih.gov/dbvar/variants/$$ urlLabel NCBI Variant Page: track dbVar_conflict superTrack dbVarSv pack compositeTrack on visibility pack itemRgb on type bigBed 9 + . html dbVarConflict shortLabel dbVar Conflict SV longLabel NCBI dbVar Curated Conflict Variants mouseOverField label searchIndex name filterLabel.overlap Variant Overlap filterValues.overlap 10 to 25,25 to 50,50 to 75,75 to 90,90 to 100 filterLabel.type Variant Type filterValues.type alu deletion,copy number gain,copy number loss,copy number variation,deletion,duplication,herv deletion,line1 deletion,sva deletion filterLabel.length Variant Length filterValues.length Under 10KB,10KB to 100KB,100KB to 1MB,Over 1MB track dbVar_conflict_pathogenic parent dbVar_conflict on shortLabel dbVar Curated Conflict SVs longLabel NCBI dbVar Curated Common SVs: Conflicts with Pathogenic bigDataUrl /gbdb/$D/bbi/dbVar/conflict_pathogenic.bb type bigBed 9 + . url https://www.ncbi.nlm.nih.gov/dbvar/variants/$$ urlLabel NCBI Variant Page: + track dbVarNr + superTrack dbVarSv pack + shortLabel dbVar NR all SV ALPHA + longLabel dbVar Non-redundant Structural Variants (DEL+DUP+INS merged, 4.6M) - ALPHA only + type bigBed 9 + + itemRgb on + release alpha + visibility hide + html dbVarNr + bigDataUrl /gbdb/$D/bbi/dbVar/nr.bb + searchIndex name + mouseOver <b>$name</b> ($svType) svLen=$svLen insLen=$insLen $binSize, count=$variantCount subsets=$subsets study=$study + filterValues.svType DEL|DEL (Deletion),DUP|DUP (Duplication),INS|INS (Insertion) + filterType.svType multipleListOr + filterLabel.svType SV Type + filter.svLen 0:248886400 + filterByRange.svLen on + filterLabel.svLen SV Length on reference (bp) + filter.insLen 0:21714506 + filterByRange.insLen on + filterLabel.insLen Insertion sequence length (bp; INS only) + filterValues.binSize small,medium,large + filterType.binSize multipleListOr + filterLabel.binSize Bin size (small <50bp, medium <1Mb, large >=1Mb) + filterValues.subsets common|in common subset,pathogenic|in pathogenic subset,somatic|in somatic subset + filterType.subsets multipleListOr + filterLabel.subsets Subset membership + filterValuesDefault.subsets common,pathogenic,somatic + filter.variantCount 1:10000 + filterByRange.variantCount on + filterLabel.variantCount Merged subvariants (number of submitted SVs at this exact placement) + url https://www.ncbi.nlm.nih.gov/dbvar/variants/$$ + urlLabel NCBI Variant Page: + skipEmptyFields on + +searchTable dbVarNr +searchMethod exact +searchType bigBed +termRegex ^[ne]ssv[0-9]+ + searchTable dbVar_common_gnomad searchMethod exact searchType bigBed termRegex ^[ne]ssv[0-9]+ searchTable dbVar_common_1000g searchMethod exact searchType bigBed termRegex ^[ne]ssv[0-9]+ searchTable dbVar_common_decipher searchMethod exact searchType bigBed termRegex ^[ne]ssv[0-9]+ searchTable dbVar_common_european searchMethod exact searchType bigBed termRegex ^[ne]ssv[0-9]+ searchTable dbVar_common_african searchMethod exact searchType bigBed termRegex ^[ne]ssv[0-9]+ searchTable dbVar_common_global searchMethod exact searchType bigBed termRegex ^[ne]ssv[0-9]+ searchTable dbVar_conflict_pathogenic searchMethod exact searchType bigBed termRegex ^[ne]ssv[0-9]+