f058c8fe4601b223ff47468eb3525c05ccd03850 max Wed Apr 22 09:17:17 2026 -0700 srSv: new short-read SV supertrack, split out of lrSv Move the three short-read SV/CNV subtracks (abelSv, onekg3202Sr, tommoJpCnv) out of the Long-read SV supertrack into a new sibling supertrack srSv (Short-read SVs), so the lrSv collection contains only long-read callsets. Filter fields (svType, svLen, insLen, AC) are mirrored at the srSv supertrack level to keep the UX parallel to lrSv. - trackDb: new human/srSv.ra with the three subtrack stanzas and updated /gbdb/$D/srSv/... bigDataUrls; corresponding stanzas removed from human/lrSv.ra. human/trackDb.ra now includes srSv.ra. Also a new human/srSv.html overview page; the SR rows and SR-specific paragraphs removed from human/lrSv.html. - Scripts: abelSv/{abelSv.as,vcfToBed.py,build.sh} and lrSv/ {lrSv1kg3202Sr*, lrSvTommoJpCnvVcfToBedGraph.py} moved to scripts/srSv/ with git mv (history preserved) and renamed to drop the "lrSv" prefix. Internal path references in abelSvBuild.sh and abelSvVcfToBed.py updated. - makeDoc: doc/hg38/abelSv.txt renamed to doc/hg38/srSv.txt and extended with the onekg3202Sr and tommoJpCnv sections moved from lrSv.txt. lrSv.txt leaves a pointer. - Data: /hive/data/genomes/hg38/bed/{abelSv,lrSv/onekg3202sr, lrSv/tommoJpCnv} moved to /hive/data/genomes/hg38/bed/srSv/*. /gbdb/hg38/lrSv/{onekg3202sr.bb,tommoJpCnv{Loss,Gain}.bw} and /gbdb/hg38/abelSv/ removed and re-linked under /gbdb/hg38/srSv/. refs #36258 diff --git src/hg/makeDb/trackDb/human/lrSv.ra src/hg/makeDb/trackDb/human/lrSv.ra index 2f553ecbf1e..777dc5bd0bd 100644 --- src/hg/makeDb/trackDb/human/lrSv.ra +++ src/hg/makeDb/trackDb/human/lrSv.ra @@ -75,111 +75,30 @@ filterByRange.svLen on filterLabel.svLen SV Length filter.insLen 0:48091 filterByRange.insLen on filterLabel.insLen Insertion Length filterByRange.alleleFreq on filterLimits.alleleFreq 0:1 filterLabel.alleleFreq Allele Frequency filter.AC 0:1816 filterByRange.AC on filterLabel.AC Allele Count skipEmptyFields on dataVersion 1.1 priority 2 - track abelSv - parent lrSv - bigDataUrl /gbdb/$D/abelSv/abelSv.bb - shortLabel CCDG 17795 SR SVs - longLabel Structural Variants from 17,795 Genomes - Illumina SHORT-READ CCDG callset (Abel et al. 2020) - included for comparison - type bigBed 9 + - itemRgb on - visibility dense - mouseOver <b>$name</b> ($svType) svLen=$svLen insLen=$insLen AF=$af AC=$AC/$an callset=$callset MSQ=$msq - skipEmptyFields on - skipFields mateChrom,matePos - filterValues.svType DEL|deletion,DUP|duplication,INV|inversion,MEI|mobile element insertion,BND|breakend/translocation - filterType.svType multipleListOr - filterLabel.svType SV Type - filterValues.callset B38|Native GRCh38 callset (14623 samples),B37lift|Lifted from GRCh37 callset (8417 samples) - filterType.callset multipleListOr - filterLabel.callset Source Callset - filterValues.filter PASS|High confidence,LOW|Low confidence - filterType.filter multipleListOr - filterLabel.filter Filter Status - filterByRange.af on - filter.af 0:1 - filterLimits.af 0:1 - filterLabel.af Allele Frequency (AF) - filterByRange.svLen on - filter.svLen 0:250000000 - filterLimits.svLen -1:250000000 - filterLabel.svLen SV Length (bp; -1 for BND) - filter.insLen 0:8545 - filterByRange.insLen on - filterLabel.insLen Insertion Length - filterByRange.msq on - filter.msq 0:500 - filterLimits.msq 0:500 - filterLabel.msq Mean Sample Quality (MSQ) - filterByRange.AC on - filter.AC 0:30000 - filterLimits.AC 0:30000 - filterLabel.AC Allele Count (AC) - url https://www.nature.com/articles/s41586-020-2371-0 - urlLabel Abel et al, Nature 2020: - - track onekg3202Sr - parent lrSv - bigDataUrl /gbdb/$D/lrSv/onekg3202sr.bb - shortLabel 1KG 3202 SR SVs - longLabel 1000 Genomes 3202-sample Illumina SHORT-READ GATK-SV callset (Byrska-Bishop 2022) - included for comparison - type bigBed 9 + - itemRgb on - visibility dense - mouseOver <b>$name</b> ($svType) svLen=$svLen insLen=$insLen AF=$alleleFreq AC=$AC/$alleleNumber popMax=$popmaxAf - filterValues.svType DEL,INS,DUP,INV,CPX,CTX,CNV - filterType.svType multipleListOr - filterLabel.svType SV Type - filter.svLen 0:154807729 - filterByRange.svLen on - filterLabel.svLen SV Length - filter.insLen 0:178243 - filterByRange.insLen on - filterLabel.insLen Insertion Length - filter.AC 0:6404 - filterByRange.AC on - filterLabel.AC Allele Count - filter.alleleFreq 0:1 - filterByRange.alleleFreq on - filterLimits.alleleFreq 0:1 - filterLabel.alleleFreq Allele Frequency (all) - filter.popmaxAf 0:1 - filterByRange.popmaxAf on - filterLimits.popmaxAf 0:1 - filterLabel.popmaxAf Population Max AF - filter.afAfr 0:1 - filterByRange.afAfr on - filterLimits.afAfr 0:1 - filterLabel.afAfr AF African - filter.afEur 0:1 - filterByRange.afEur on - filterLimits.afEur 0:1 - filterLabel.afEur AF European - skipEmptyFields on - track gustafsonSv parent lrSv bigDataUrl /gbdb/$D/lrSv/gustafson.bb shortLabel 1KG ONT 100 SVs longLabel Structural Variants from 100 1000 Genomes ONT Samples (Gustafson et al. 2024) type bigBed 9 + itemRgb on visibility dense mouseOver <b>$name</b> ($svType) svLen=$svLen insLen=$insLen AC=$AC samples=$sampleCount filterValues.svType DEL,INS,DUP,INV filterType.svType multipleListOr filterLabel.svType SV Type filter.svLen 0:98289 filterByRange.svLen on filterLabel.svLen SV Length @@ -246,63 +165,30 @@ filterByRange.insLen on filterLabel.insLen Insertion Length filter.AC 0:1890 filterByRange.AC on filterLabel.AC Allele Count (approx 2*SUPP) filter.sampleCount 1:945 filterByRange.sampleCount on filterLabel.sampleCount Number of Supporting Samples filter.alleleFreq 0:1 filterByRange.alleleFreq on filterLimits.alleleFreq 0:1 filterLabel.alleleFreq Allele Frequency skipEmptyFields on urls chr2="hgTracks?position=$$" - track tommoJpCnv - parent lrSv - container multiWig - aggregate transparentOverlay - showSubtrackColorOnUi on - shortLabel ToMMo 48K CNV SR - longLabel CNV Carrier Counts from 48,874 Japanese Individuals (ToMMo 48KJPN-CNV, short-read WGS; 1 kb bins) - included for comparison - type bigWig 0 48874 - autoScale on - viewLimits 0:1000 - viewLimitsMax 0:48874 - maxHeightPixels 100:32:8 - visibility full - priority 2.5 - - track tommoJpCnvLoss - parent tommoJpCnv - bigDataUrl /gbdb/$D/lrSv/tommoJpCnvLoss.bw - shortLabel ToMMo CNV Loss - longLabel Samples with copy-number loss (CN<2) per 1 kb bin, ToMMo 48KJPN-CNV - type bigWig 0 48874 - color 200,0,0 - altColor 200,0,0 - - track tommoJpCnvGain - parent tommoJpCnv - bigDataUrl /gbdb/$D/lrSv/tommoJpCnvGain.bw - shortLabel ToMMo CNV Gain - longLabel Samples with copy-number gain (CN>2) per 1 kb bin, ToMMo 48KJPN-CNV - type bigWig 0 48874 - color 0,160,0 - altColor 0,160,0 - track tommoJpSv parent lrSv bigDataUrl /gbdb/$D/lrSv/tommoJp.bb shortLabel ToMMo 333 SVs longLabel Structural Variants from 333 Japanese Individuals (ToMMo, 111 Trios) type bigBed 9 + itemRgb on visibility dense mouseOver <b>$name</b> ($svType) svLen=$svLen insLen=$insLen AF=$alleleFreq AC=$AC filterValues.svType DEL,INS filterType.svType multipleListOr filterLabel.svType SV Type filter.svLen 0:99985 filterByRange.svLen on filterLabel.svLen SV Length