e6bcec351aa8f5bc7218e8862e15c149aadb3479 lrnassar Fri Jul 10 12:18:40 2026 -0700 lrSv: complete the longReadVariants rename - reparent subtracks and update refs. refs #36258 Completes the previous rename commit (which carried only the colorsDbLegacy file moves). Renames "track lrSv" to "track longReadVariants" in lrSv.ra (adds "html lrSv" to keep the existing description page), reparents all subtracks plus the merged lrSvAll and its lrSvMergeAll.py generator, and updates the hs1 override, relatedTracks.ra, and the mei/meiHgsvc3/srSv/lrSvAll cross-links. Retitles the retired colorsDbLegacy track and reparents its subtracks. Only the internal track name changes; subtrack names, /gbdb/$D/lrSv/ data paths, and the lrSv.ra filename are unchanged. diff --git src/hg/makeDb/trackDb/relatedTracks.ra src/hg/makeDb/trackDb/relatedTracks.ra index 7caab13856c..f3c59684c3f 100644 --- src/hg/makeDb/trackDb/relatedTracks.ra +++ src/hg/makeDb/trackDb/relatedTracks.ra @@ -93,42 +93,42 @@ mm39 knownGene knownGeneArchive View previous versions of GENCODE Genes mm39 knownGeneArchive knownGene View the latest GENCODE Genes version # mm10 ENCODE4 Regulation: mm10 encode4Reg encode3Reg Previous ENCODE3 Regulation track mm10 encode3Reg encode4Reg New ENCODE4 Regulation track mm10 encode4Reg cCREs Related ENCODE4 cCRE annotations mm10 cCREs encode4Reg Related ENCODE4 regulation data mm10 mouseDevTimecourse encode3Reg Related ENCODE3 Regulation tracks mm10 encode3Reg mouseDevTimecourse Related ENCODE Expression track mm10 mouseDevTimecourse encode4Reg Related ENCODE4 Regulation tracks mm10 encode4Reg mouseDevTimecourse Related ENCODE Expression track # hg38 long-read SV supertrack cross-links to other SV resources: -hg38 lrSv gnomadStructuralVariants Short-read structural variants from gnomAD v4.1 -hg38 gnomadStructuralVariants lrSv Long-read structural variants across multiple cohorts -hg38 lrSv dbVarSv NCBI dbVar structural variants (short-read and long-read, germline and clinical) -hg38 dbVarSv lrSv Long-read structural variants across multiple cohorts -hg38 lrSv dgvPlus Database of Genomic Variants (DGV) structural variation catalog -hg38 dgvPlus lrSv Long-read structural variants across multiple cohorts -hg38 lrSv giabSv Genome in a Bottle high-confidence SV benchmark callsets -hg38 giabSv lrSv Long-read structural variants across multiple cohorts -hg38 lrSv mei Polymorphic Mobile Element Insertions (Alu, L1, SVA, HERVK, snRNA) from HGSVC3 long-read assemblies -hg38 mei lrSv Long-read structural variants across multiple cohorts (parent SV callsets for the HGSVC3 MEI track) -hs1 lrSv mei Polymorphic Mobile Element Insertions (Alu, L1, SVA, HERVK, snRNA) from HGSVC3 long-read assemblies -hs1 mei lrSv Long-read structural variants across multiple cohorts (parent SV callsets for the HGSVC3 MEI track) +hg38 longReadVariants gnomadStructuralVariants Short-read structural variants from gnomAD v4.1 +hg38 gnomadStructuralVariants longReadVariants Long-read structural variants across multiple cohorts +hg38 longReadVariants dbVarSv NCBI dbVar structural variants (short-read and long-read, germline and clinical) +hg38 dbVarSv longReadVariants Long-read structural variants across multiple cohorts +hg38 longReadVariants dgvPlus Database of Genomic Variants (DGV) structural variation catalog +hg38 dgvPlus longReadVariants Long-read structural variants across multiple cohorts +hg38 longReadVariants giabSv Genome in a Bottle high-confidence SV benchmark callsets +hg38 giabSv longReadVariants Long-read structural variants across multiple cohorts +hg38 longReadVariants mei Polymorphic Mobile Element Insertions (Alu, L1, SVA, HERVK, snRNA) from HGSVC3 long-read assemblies +hg38 mei longReadVariants Long-read structural variants across multiple cohorts (parent SV callsets for the HGSVC3 MEI track) +hs1 longReadVariants mei Polymorphic Mobile Element Insertions (Alu, L1, SVA, HERVK, snRNA) from HGSVC3 long-read assemblies +hs1 mei longReadVariants Long-read structural variants across multiple cohorts (parent SV callsets for the HGSVC3 MEI track) # EVE cross-links: hg38 eve alphaMissense AlphaMissense, a similar deep-learning missense pathogenicity predictor hg38 alphaMissense eve EVE, a missense pathogenicity predictor trained on evolutionary sequence variation hg38 eve primateAi PrimateAI-3D, a similar deep-learning missense pathogenicity predictor using primate variation hg38 primateAi eve EVE, a missense pathogenicity predictor trained on evolutionary sequence variation hg38 eve revel REVEL, an ensemble missense pathogenicity score built from multiple predictors hg38 revel eve EVE, a missense pathogenicity predictor trained on evolutionary sequence variation hg38 eve clinPred ClinPred, an ensemble missense pathogenicity predictor that incorporates gnomAD allele frequency hg38 clinPred eve EVE, a missense pathogenicity predictor trained on evolutionary sequence variation # PrimateAI-3D cross-links: hg38 primateAi alphaMissense AlphaMissense, a similar deep-learning missense pathogenicity predictor hg38 alphaMissense primateAi PrimateAI-3D, a similar deep-learning missense pathogenicity predictor using primate variation hg38 primateAi revel REVEL, an ensemble missense pathogenicity score built from multiple predictors