6a29bc1077e1bd2926fa1508c6fdde383397f4a4 mspeir Tue Sep 8 16:14:56 2026 -0700 relatedTracks.ra: drop 20 entries naming tracks that are not on the RR An audit of the table against the public trackDb found 77 relationship rows pointing at a track the RR does not have. Most are fine and stay: the track is either gated behind an alpha include and still in development (LCRs, gerp, imprinting, mei, srSv, t2tChain, tads, TOGAv2, clinvarMapped, colorsDbLegacy, hg38Patch11, singleCellSignalsPeaks, cancerMutations), or the family is already public on other assemblies and only this version or assembly has yet to be pushed (transMapV6, crispr10K, tanDups, ukbDepletion). Those entries start working on their own when the track ships. The 20 lines removed here name tracks with no public counterpart under any name on any assembly, so they could never render for a reader on the RR: ucscRetroAli8, superseded by the V9 track that is public wgRnaOld and cancerMutations, both release alpha transMapV4, absent from the RR entirely, so the source page does not exist ensGene on hg38 and mm10, where Ensembl Genes was retired sibAltEvents, public on no assembly chainNetHs1, which is assembly-hub machinery rather than a native hg38 track cloneEndUcsc, a mapping that only ever existed on hgwdev The three crispr lines came out for a different reason. On hgwdev crispr is a superTrack over crisprRanges and crisprTargets while the RR carries only the standalone crisprAllTargets, so the entries looked like they wanted repointing. The file already relates crisprAllTargets and crispr10K reciprocally further down, on all three assemblies, which made them redundant instead. Every name still in the file resolves in the hgwdev trackDb, and no duplicate assembly and track pair remains. Rebuilt with make update on hg38, hg19 and mm10: 24 rows dropped, none added, nothing else changed. The original audit checked names against alpha, which is why these got in. refs #38016 Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> diff --git src/hg/makeDb/trackDb/relatedTracks.ra src/hg/makeDb/trackDb/relatedTracks.ra index 97cea089e65..62c7ece2f1f 100644 --- src/hg/makeDb/trackDb/relatedTracks.ra +++ src/hg/makeDb/trackDb/relatedTracks.ra @@ -208,64 +208,52 @@ hg19 cnvDevDelay dosageSensitivity Predicted gene-level haploinsufficiency (pHaplo) and triplosensitivity (pTriplo) scores from Collins et al. 2022 for genes within these CNVs # danRer11 BAC clone tracks: danRer11 bacEndPairsLift choriCloneEnds CHORI zebrafish BAC clone end placements (CH73, CH211, CH1073) from NCBI Clone DB on GRCz11 danRer11 choriCloneEnds bacEndPairsLift Zebrafish BAC end pairs lifted from danRer4 (older UCSC BLAT placements) # Relationships added from the #38016 audit. Version successions run one way, # from the older track to the newer one; archives are reciprocal. # Version successions, from the older track to the newer one: hg38 >caddSuper caddSuper1_7 The newer CADD release, with an updated model and training set hg38 >cosmicRegions cosmicMuts Individual somatic mutations from the current COSMIC release (V101) hg38 dbSnp155Composite dbSnpArchive Older dbSNP builds, kept for reproducing earlier analyses hg38 dbSnpArchive dbSnp155Composite The dbSNP release currently used by the Browser hg38 >gtexGene gtexGeneV8 The newer GTEx release, 54 tissues from 948 donors -hg38 >ucscRetroAli8 ucscRetroAli9 The newer version of this track -hg38 >wgRnaOld wgRna The newer version of this track hg38 >covidHgiGwas covidHgiGwasR4Pval A later release of the same COVID-19 Host Genetics Initiative meta-analysis hg38 >colorsDbLegacy longReadVariants Current long-read structural variant callsets, including the up-to-date CoLoRSdb release -hg38 >crispr crispr10K The same target sites computed over a wider window, exons plus 10 kb rather than 200 bp -hg38 >transMapV4 transMapV6 The current version of the TransMap alignments hg38 >transMapV5 transMapV6 The current version of the TransMap alignments hg38 knownGeneArchive wgEncodeGencodeSuper All transcripts from each GENCODE release, including sets never used as the default gene track hg38 wgEncodeGencodeSuper knownGeneArchive Previous default gene tracks, one per GENCODE release hg38 >genePredArchive knownGene The current default gene set -hg38 >ensGene knownGene The current GENCODE gene set, which shares its annotation with Ensembl hg19 >caddSuper caddSuper1_7 The newer CADD release, with an updated model and training set hg19 >cosmicRegions cosmicMuts Individual somatic mutations from the current COSMIC release (V101) hg19 dbSnp155Composite dbSnpArchive Older dbSNP builds, kept for reproducing earlier analyses hg19 dbSnpArchive dbSnp155Composite The dbSNP release currently used by the Browser hg19 >gtexGene gtexGeneV8 The newer GTEx release, 54 tissues from 948 donors -hg19 >wgRnaOld wgRna The newer version of this track hg19 >covidHgiGwas covidHgiGwasR4Pval A later release of the same COVID-19 Host Genetics Initiative meta-analysis -hg19 >crispr crispr10K The same target sites computed over a wider window, exons plus 10 kb rather than 200 bp -hg19 >transMapV4 transMapV6 The current version of the TransMap alignments hg19 >transMapV5 transMapV6 The current version of the TransMap alignments hg19 knownGeneArchive wgEncodeGencodeSuper All transcripts from each GENCODE release, including sets never used as the default gene track hg19 wgEncodeGencodeSuper knownGeneArchive Previous default gene tracks, one per GENCODE release hg19 >genePredArchive knownGene The current default gene set -hg19 >ensGene knownGene The current GENCODE gene set, which shares its annotation with Ensembl mm39 knownGeneArchive wgEncodeGencodeSuper All transcripts from each GENCODE release, including sets never used as the default gene track mm39 wgEncodeGencodeSuper knownGeneArchive Previous default gene tracks, one per GENCODE release -mm10 >crispr crispr10K The same target sites computed over a wider window, exons plus 10 kb rather than 200 bp -mm10 >transMapV4 transMapV6 The current version of the TransMap alignments mm10 >transMapV5 transMapV6 The current version of the TransMap alignments -mm10 >ensGene knownGene The current GENCODE gene set, which shares its annotation with Ensembl # Clinical variant database cross-links: hg38 clinvar hgmd Disease-causing mutations curated from the literature by HGMD; the public release lags the licensed version hg38 hgmd clinvar Variant interpretations submitted by clinical laboratories, with review status and conflicts hg38 clinvar lovdComp Variants collected in the gene-specific Leiden Open Variation Database instances hg38 lovdComp clinvar Variant interpretations submitted by clinical laboratories worldwide hg38 clinvar decipherContainer Patient variants and CNVs from the DECIPHER developmental disorder database hg38 decipherContainer clinvar Variant interpretations submitted by clinical laboratories, with review status hg38 clinvarMapped clinvar The original, directly submitted ClinVar variant records hg38 clinvar clinvarMapped Coding variants projected onto paralogous loci by sequence homology hg38 mitoMap nuMtSeq Mitochondrial segments inserted into the nuclear genome, a common source of false-positive chrM variant calls hg38 nuMtSeq mitoMap Variants and annotations on the mitochondrial genome itself hg19 clinvar hgmd Disease-causing mutations curated from the literature by HGMD; the public release lags the licensed version hg19 hgmd clinvar Variant interpretations submitted by clinical laboratories, with review status and conflicts @@ -401,90 +389,82 @@ hg38 ucscGenePfam uniprot Protein domains and functional sites from UniProt hg38 uniprot ucscGenePfam Pfam domains mapped onto GENCODE transcripts hg38 knownGene mane One representative transcript per gene, agreed between RefSeq and GENCODE hg38 mane knownGene The full GENCODE gene set that MANE Select transcripts are drawn from hg38 refSeqComposite mane The MANE Select subset of RefSeq transcripts, matched to GENCODE hg38 mane refSeqComposite The full NCBI RefSeq transcript set that MANE Select is drawn from hg38 knownGene hgnc Official gene symbols and names from the HGNC, with previous symbols and aliases hg38 hgnc knownGene The default gene set, whose gene names come from this nomenclature hg38 refSeqComposite hgnc Official gene symbols and names from the HGNC, with previous symbols and aliases hg38 hgnc refSeqComposite Transcript annotations from NCBI, which use these gene symbols hg38 mane hgnc Official gene symbols and names from the HGNC, with previous symbols and aliases hg38 hgnc mane One agreed representative transcript per gene, matched between RefSeq and GENCODE hg38 >ccdsGene mane One representative transcript per gene, matched between RefSeq and GENCODE hg38 refSeqComposite xenoRefGene RefSeq transcripts from other species, aligned to the human genome hg38 xenoRefGene refSeqComposite Human RefSeq transcripts, rather than transcripts from other species -hg38 ~knownAlt sibAltEvents Another set of alternative splicing and promoter events called from transcript alignments -hg38 sibTxGraph sibAltEvents Individual alternative splicing and polyadenylation events derived from this graph -hg38 sibAltEvents sibTxGraph The full alternative splicing graph these events are derived from hg38 pseudogenes ucscRetroAli9 Retroposed gene copies, a major source of processed pseudogenes hg38 ucscRetroAli9 pseudogenes Curated pseudogene annotations from GENCODE and Yale hg38 ncOrfs gwipsvizRiboseq Ribosome profiling data, the main evidence for translation of non-canonical ORFs hg38 gwipsvizRiboseq ncOrfs Open reading frames outside annotated CDS regions, called partly from ribosome profiling hg38 lrg lrgTranscriptAli The fixed LRG transcript annotations within these regions hg38 lrgTranscriptAli lrg The genomic LRG reference regions these transcripts belong to hg38 crispr10K crisprAllTargets Cas9 target sites across the whole genome, not only near exons hg38 crisprAllTargets crispr10K Cas9 target sites restricted to exons and 10 kb of flanking sequence hg19 uniprot spMut Amino acid substitutions annotated in UniProt, mapped to the genome hg19 spMut uniprot Protein domains, sites and other UniProt annotations mapped to the genome hg19 ucscGenePfam uniprot Protein domains and functional sites from UniProt hg19 uniprot ucscGenePfam Pfam domains mapped onto GENCODE transcripts hg19 knownGene hgnc Official gene symbols and names from the HGNC, with previous symbols and aliases hg19 hgnc knownGene The default gene set, whose gene names come from this nomenclature hg19 refSeqComposite hgnc Official gene symbols and names from the HGNC, with previous symbols and aliases hg19 hgnc refSeqComposite Transcript annotations from NCBI, which use these gene symbols hg19 refSeqComposite xenoRefGene RefSeq transcripts from other species, aligned to the human genome hg19 xenoRefGene refSeqComposite Human RefSeq transcripts, rather than transcripts from other species -hg19 ~knownAlt sibAltEvents Another set of alternative splicing and promoter events called from transcript alignments -hg19 sibTxGraph sibAltEvents Individual alternative splicing and polyadenylation events derived from this graph -hg19 sibAltEvents sibTxGraph The full alternative splicing graph these events are derived from hg19 lrg lrgTranscriptAli The fixed LRG transcript annotations within these regions hg19 lrgTranscriptAli lrg The genomic LRG reference regions these transcripts belong to hg19 crispr10K crisprAllTargets Cas9 target sites across the whole genome, not only near exons hg19 crisprAllTargets crispr10K Cas9 target sites restricted to exons and 10 kb of flanking sequence mm39 ucscGenePfam uniprot Protein domains and functional sites from UniProt mm39 uniprot ucscGenePfam Pfam domains mapped onto GENCODE transcripts mm39 refSeqComposite xenoRefGene RefSeq transcripts from other species, aligned to the human genome mm39 xenoRefGene refSeqComposite Human RefSeq transcripts, rather than transcripts from other species mm10 uniprot spMut Amino acid substitutions annotated in UniProt, mapped to the genome mm10 spMut uniprot Protein domains, sites and other UniProt annotations mapped to the genome mm10 ucscGenePfam uniprot Protein domains and functional sites from UniProt mm10 uniprot ucscGenePfam Pfam domains mapped onto GENCODE transcripts mm10 refSeqComposite xenoRefGene RefSeq transcripts from other species, aligned to the human genome mm10 xenoRefGene refSeqComposite Human RefSeq transcripts, rather than transcripts from other species mm10 crispr10K crisprAllTargets Cas9 target sites across the whole genome, not only near exons mm10 crisprAllTargets crispr10K Cas9 target sites restricted to exons and 10 kb of flanking sequence hs1 refSeqComposite xenoRefGene RefSeq transcripts from other species, aligned to the human genome hs1 xenoRefGene refSeqComposite Human RefSeq transcripts, rather than transcripts from other species danRer11 refSeqComposite xenoRefGene RefSeq transcripts from other species, aligned to the human genome danRer11 xenoRefGene refSeqComposite Human RefSeq transcripts, rather than transcripts from other species # Map and assembly cross-links: -hg38 ~t2tChain chainNetHs1 Another alignment of the T2T CHM13 assembly to GRCh38 hg38 ~t2tChain chm13LiftOver Another alignment of the T2T CHM13 assembly to GRCh38 hg38 problematic LCRs Low-complexity regions measured by longdust, another common source of alignment artifacts hg38 LCRs problematic Curated regions that often cause artifacts in sequencing and alignment hg38 hg38Patch11 patchesPsl Alignments of the patch and alt sequences to the primary assembly hg38 patchesPsl hg38Patch11 The patch and alternate sequences themselves, as placed on the assembly hg38 exomeProbesets genotypeArrays Microarray probesets and optical genome mapping sites hg38 genotypeArrays exomeProbesets Exome capture kit target regions and probe positions -hg38 ~cloneEndSuper cloneEndUcsc Another mapping of the same clone library end sequences hg19 exomeProbesets genotypeArrays Microarray probesets and optical genome mapping sites hg19 genotypeArrays exomeProbesets Exome capture kit target regions and probe positions hs1 problematic LCRs Low-complexity regions measured by longdust, another common source of alignment artifacts hs1 LCRs problematic Curated regions that often cause artifacts in sequencing and alignment # Comparative genomics cross-links: hg38 unusualcons cons100way The vertebrate conservation scores these unusually conserved regions are called from hg38 cons100way unusualcons Ultraconserved elements, human accelerated regions and similar features hg38 gerp cons100way UCSC conservation scores from a 100-species vertebrate alignment hg38 cons100way gerp Conservation scores from Ensembl, computed on a 65-amniote alignment hg38 ~cons241way cons447way Another Zoonomia mammalian alignment, built on a different species set # Mouse gene and regulation cross-links: