7e87cadb469b4e0eb4fb7f973154357cfe7fc345 lrnassar Mon Sep 21 15:56:18 2026 -0700 QA fixes for the mei (Mobile Insertions) track collection. refs #37524 Fix two data bugs found during QA and rebuild the affected bigBeds. meiEul1dbToBed.py looked up samples and individuals by name, but euL1db joins on 1-based row numbers, so neither join ever matched and the individual count, tissues, clinical conditions and populations were empty on all 8,991 insertions while the contributing-samples table printed row numbers. Both loaders now key on the row number, the table prints the sample name, and the adjacent population filter is case-insensitive so it actually drops "unknown". meiHgsvc3CsvToBed.py took alt[1:] on every record, which dropped the first base of the element on the 96 GRCh38 and 111 T2T-CHM13 records where PALMER2 is the only caller and ALT carries no anchor base; it now prefers INFO SEQ, which always matches SVLEN. Correct seven statements on the description pages against their sources: the HGSVC3 single-caller split was attributed to PALMER rather than L1ME-AID, its orthogonal concordance was 90.8% rather than 92.5%, euL1db was credited with aligning the L1HS consensus when the paper says it was processed from our RepeatMasker track, DeepMEI's network was described as a classifier rather than a genotyper and given the wrong training set, euL1db listed two detection methods absent from the data, and HMEID contradicted itself on the MELT ASSESS cutoff. Also: the SweGen bigDataUrl now points at _swegen.bb so the restricted callset is kept off the download server; the container page no longer claims the whole collection is long-read, lists the two euL1db subtracks, scopes its display conventions to the subtracks they describe, and cites all six papers; dead and wrong track links are repointed and pinned to a db; $db replaces hardcoded hg38 in paths on pages that serve three assemblies; the euL1db labels no longer carry hg38 counts and a lift note that made no sense on hg19; all six subtracks gain a dataVersion; the euL1db filter ranges match the data; and five autoSql field descriptions match what the files contain. Document the gbdb symlinks and the QA changes in doc/hg38/mei.txt, correct the HMEID bedToBigBed type there, and add an hg19.txt pointer since hg19 carries the two euL1db subtracks. diff --git src/hg/makeDb/trackDb/human/mei.ra src/hg/makeDb/trackDb/human/mei.ra index bfe5d2431c3..1bdaecd748c 100644 --- src/hg/makeDb/trackDb/human/mei.ra +++ src/hg/makeDb/trackDb/human/mei.ra @@ -1,27 +1,28 @@ track mei superTrack on shortLabel Mobile Insertions -longLabel Mobile Element Insertions (Polymorphic) +longLabel Mobile element insertions (polymorphic) group varRep visibility hide track meiHgsvc3 parent mei bigDataUrl /gbdb/$D/mei/hgsvc3.bb shortLabel HGSVC3 65 MEIs - longLabel Mobile Element Insertions in 65 HGSVC3 Long-Read Assembled Samples + longLabel Mobile element insertions in 65 HGSVC3 long-read assembled samples + dataVersion HGSVC3 Mobile Elements release 1.0, 2024-12-11 type bigBed 9 + itemRgb on visibility pack mouseOver ${teClass} insertion (${svLen} bp)
Carriers: ${carrierCount}/${sampleCount} samples
Allele frequency: ${altAlleleFreq}
Callers: ${callerCount}/2 (PALMER ${palmer}, L1ME-AID ${l1meAid}) filterValues.teClass Alu,L1,SVA,HERVK,snRNA filterType.teClass multipleListOr filterLabel.teClass Mobile Element Class filter.svLen 0:9478 filterByRange.svLen on filterLabel.svLen Insertion Length (bp) filter.altAlleleFreq 0:1 filterByRange.altAlleleFreq on filterLimits.altAlleleFreq 0:1 filterLabel.altAlleleFreq Allele Frequency filter.carrierCount 0:65 @@ -37,128 +38,133 @@ filterType.palmer multipleListOr filterLabel.palmer PALMER Validated filterValues.refTrf True,False filterType.refTrf multipleListOr filterLabel.refTrf In Tandem Repeat filter.refSegDup 0:1 filterByRange.refSegDup on filterLimits.refSegDup 0:1 filterLabel.refSegDup Segmental Duplication Overlap skipEmptyFields on track meiDeepmei1kg parent mei bigDataUrl /gbdb/$D/mei/deepmei1kg.bb shortLabel DeepMEI 1000G MEIs - longLabel Mobile Element Insertions in 3,202 1000 Genomes Samples (DeepMEI) + longLabel Mobile element insertions in 3,202 1000 Genomes samples (DeepMEI) + dataVersion DeepMEI 1000 Genomes high-confidence callset, 2022-11-21 type bigBed 9 + itemRgb on visibility pack mouseOver ${teClass} insertion
Carriers: ${carrierCount}/${sampleCount} samples
Allele frequency: ${altAlleleFreq} filterValues.teClass Alu,L1,SVA filterType.teClass multipleListOr filterLabel.teClass Mobile Element Class filter.altAlleleFreq 0:1 filterByRange.altAlleleFreq on filterLimits.altAlleleFreq 0:1 filterLabel.altAlleleFreq Allele Frequency filter.carrierCount 0:3202 filterByRange.carrierCount on filterLabel.carrierCount Carrier Sample Count track meiHmeid parent mei bigDataUrl /gbdb/$D/mei/hmeid.bb shortLabel HMEID 5675 MEIs - longLabel Mobile Element Insertions in 5,675 NyuWa + 1000 Genomes Samples (HMEID v1.1) + longLabel Mobile element insertions in 5,675 NyuWa + 1000 Genomes samples (HMEID v1.1) + dataVersion HMEID v1.1 type bigBed 9 + itemRgb on visibility pack mouseOver ${teClass} insertion (${svLen} bp)
Carrier haplotypes: ${altAlleleCount}/${alleleNumber}
Allele frequency: ${altAlleleFreq}
NyuWa AF: ${nyuwaAF}, 1KGP AF: ${kgpAF}
MELT ASSESS: ${assess}/5 filterValues.teClass Alu,L1,SVA,HERVK filterType.teClass multipleListOr filterLabel.teClass Mobile Element Class filter.svLen -1:8757 filterByRange.svLen on filterLabel.svLen Insertion Length (bp, -1 if unknown) filter.altAlleleFreq 0:1 filterByRange.altAlleleFreq on filterLimits.altAlleleFreq 0:1 filterLabel.altAlleleFreq Allele Frequency (all) filter.nyuwaAF 0:1 filterByRange.nyuwaAF on filterLimits.nyuwaAF 0:1 filterLabel.nyuwaAF NyuWa Allele Frequency filter.kgpAF 0:1 filterByRange.kgpAF on filterLimits.kgpAF 0:1 filterLabel.kgpAF 1KGP Allele Frequency filterValues.assess 3,4,5 filterType.assess multipleListOr filterLabel.assess MELT ASSESS Score track meiEul1db parent mei bigDataUrl /gbdb/$D/mei/eul1db.bb shortLabel euL1db Insertions - longLabel euL1db: 8,988 curated L1-HS Insertion Polymorphisms (Mir 2015, lifted from hg19) + longLabel euL1db: curated L1-HS insertion polymorphisms (Mir 2015) + dataVersion euL1db v1.00, 2014-10-14 type bigBed 9 + itemRgb on visibility pack mouseOver ${name}
Lineage: ${lineage}
Sub-group: ${subGroups}
Integrity: ${integrity}
Pseudo-AF: ${pseudoAlleleFreq}
SRIPs: ${sripCount} from ${sampleCount} samples in ${studyCount} studies
Gene: ${gene} filter.pseudoAlleleFreq 0:1 filterByRange.pseudoAlleleFreq on filterLimits.pseudoAlleleFreq 0:1 filterLabel.pseudoAlleleFreq Pseudo-allele frequency - filter.sripCount 0:1000 + filter.sripCount 0:675 filterByRange.sripCount on filterLabel.sripCount SRIP count (sample observations) - filter.studyCount 0:30 + filter.studyCount 0:10 filterByRange.studyCount on filterLabel.studyCount Study count filterValues.lineage germline,somatic,germline\,somatic,unknown filterType.lineage multipleListOr filterLabel.lineage Lineage filterValues.pcrValidated yes,no filterType.pcrValidated multipleListOr filterLabel.pcrValidated PCR validated filterValues.inReferenceL1HS yes,no filterType.inReferenceL1HS multipleListOr filterLabel.inReferenceL1HS In reference L1HS skipEmptyFields on track meiEul1dbRef parent mei bigDataUrl /gbdb/$D/mei/eul1dbRef.bb shortLabel euL1db Ref L1HS - longLabel euL1db: 1,540 L1-HS Copies Present in the Reference Genome (lifted from hg19) + longLabel euL1db: L1-HS copies present in the reference genome (Mir 2015) + dataVersion euL1db v1.00, 2014-10-14 type bigBed 9 + itemRgb on visibility hide mouseOver ${subGroup}
Integrity: ${integrity}
L1HS consensus: ${refStart}-${refStop}
Length: ${elementLen} bp filterValues.subGroup L1HS-Ta,L1HS-PreTa,L1HS-undef filterType.subGroup multipleListOr filterLabel.subGroup L1HS sub-group filterValues.integrity full-length,5prime-truncated,3prime-truncated,internal_fragment filterType.integrity multipleListOr filterLabel.integrity Integrity track meiSwegen parent mei - bigDataUrl /gbdb/$D/mei/swegen.bb + bigDataUrl /gbdb/$D/mei/_swegen.bb shortLabel SweGen 1000 MEIs - longLabel Mobile Element Insertions in 1,000 SweGen Swedish Samples (MELT, lifted from GRCh37) + longLabel Mobile element insertions in 1,000 SweGen Swedish samples (MELT, lifted from GRCh37) + dataVersion SweGen MELT callset, 2018-03-14 type bigBed 9 + itemRgb on visibility pack tableBrowser off mouseOver ${teClass} insertion (${svLen} bp, ${meiSubfamily})
Allele count: ${altAlleleCount} of ~2000
Allele frequency: ${altAlleleFreq}
MELT ASSESS: ${assess}/5
FILTER: ${filterStatus} filterValues.teClass Alu,L1,SVA,HERVK filterType.teClass multipleListOr filterLabel.teClass Mobile Element Class filter.svLen -1:8757 filterByRange.svLen on filterLabel.svLen Insertion Length (bp, -1 if unknown) filter.altAlleleFreq 0:1 filterByRange.altAlleleFreq on filterLimits.altAlleleFreq 0:1 filterLabel.altAlleleFreq Allele Frequency