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/scripts/mei/meiHgsvc3.as src/hg/makeDb/scripts/mei/meiHgsvc3.as index b732e266a3f..f2e5bea31bb 100644 --- src/hg/makeDb/scripts/mei/meiHgsvc3.as +++ src/hg/makeDb/scripts/mei/meiHgsvc3.as @@ -1,29 +1,29 @@ table meiHgsvc3 "Novel Mobile Element Insertions in 65 HGSVC3 long-read assembled samples (vs GRCh38)" ( string chrom; "Reference chromosome or scaffold" uint chromStart; "0-based start position (anchor base)" uint chromEnd; "Half-open end position (anchor base + 1)" -string name; "Item label (INS, insertion length, carrier sample count)" +string name; "Item label (element class, insertion length, carrier sample count)" uint score; "Score (alt-allele frequency * 1000)" char[1] strand; "Strand (always .)" uint thickStart; "Start of thick drawing region" uint thickEnd; "End of thick drawing region" uint itemRgb; "RGB color, by mobile-element class" string teClass; "TE class|Family of mobile element (Alu, L1, SVA, HERVK, snRNA)" string teType; "Repeat designation|Repeat designation as reported in source (e.g. SINE/Alu)" int svLen; "Insertion length (bp)" int altAlleleCount; "Carrier haplotypes|Haplotypes carrying the insertion" int alleleNumber; "Genotyped haplotypes|Total haplotypes successfully genotyped" float altAlleleFreq; "Allele frequency|Fraction of genotyped haplotypes carrying the insertion" int carrierCount; "Carrier samples|Samples with at least one insertion allele" int sampleCount; "Genotyped samples|Samples with at least one called haplotype" string sourceSample; "Discovery sample|Sample-haplotype in which the insertion was originally called" int callerCount; "Caller count|Number of MEI callers supporting this insertion (1 or 2)" string l1meAid; "L1ME-AID validated|Whether the insertion was validated by L1ME-AID (Yes/No)" string palmer; "PALMER validated|Whether the insertion was validated by PALMER (Yes/No)" float refSegDup; "Segmental dup. overlap|Fraction of insertion site overlapping reference segmental duplications (REF_SD)" string refTrf; "Tandem repeat|Insertion site overlaps a reference tandem repeat (REF_TRF)" lstring carrierSamples; "Carrier sample list|Comma-separated list of samples with at least one insertion allele" lstring insertSeq; "Inserted sequence|DNA sequence of the inserted mobile element (ALT allele minus the anchor base)" )