da5860e01a546d10d1276880758dcfaa8e573467 mspeir Fri Sep 4 10:24:18 2026 -0700 relatedTracks.ra: connect RepeatMasker, GWAS Catalog, HGNC and CRISPR Follow-up to the #38016 audit, which organized its work by writing one reason template per cluster of tracks. That approach only linked a track if it matched some cluster's phrasing, so tracks that are conceptually adjacent but described differently were skipped. Four such cases, all of which had no related tracks at all before this: RepeatMasker. The audit's repeat cluster was written around tandem repeats, so rmsk, which annotates interspersed repeats, fell outside the wording. It is one of the most widely used tracks in the browser and had nothing. Now relates to Interrupted Repeats and RepeatMasker Visualization, which are derived from it, to Simple Repeats as the tandem counterpart, and to WindowMasker + SDust as the library-free alternative. GWAS Catalog, SNPedia and Variants in Papers. The audit built a cluster for variant impact prediction and another for gene-disease curation, but none for variants reported in the literature, so all three were left isolated. GWAS Catalog also now relates to the GTEx cis-eQTLs, since looking for the gene behind an association signal is a common reason to open either one. HGNC. The gene symbol authority, unlinked from the gene tracks that use its nomenclature. Now relates to GENCODE, NCBI RefSeq and MANE. CRISPR. The 200 bp window track is superseded by the 10 kb one, computed by the same pipeline over a wider region, so it links forward to it and not back, the same rule the audit applies to other version successions. Counts: 32 relationships, 70 lines, taking the file to 487 relationship lines. 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 148bc8a254b..97cea089e65 100644 --- src/hg/makeDb/trackDb/relatedTracks.ra +++ src/hg/makeDb/trackDb/relatedTracks.ra @@ -212,54 +212,57 @@ 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 @@ -389,49 +392,59 @@ mm10 cCREs refSeqFuncElems Regulatory and other functional elements curated by NCBI from the literature mm10 refSeqFuncElems cCREs Candidate regulatory elements called from ENCODE chromatin data danRer11 cpgIslandSuper dnaMethylation Measured methylation levels, which are often depleted over these islands danRer11 dnaMethylation cpgIslandSuper CpG-dense regions predicted from the reference sequence # Gene and protein cross-links: hg38 uniprot spMut Amino acid substitutions annotated in UniProt, mapped to the genome hg38 spMut uniprot Protein domains, sites and other UniProt annotations mapped to the genome 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 @@ -488,30 +501,87 @@ mm10 tabulaMurisSenis tabulaMuris Single-cell expression across adult mouse organs, the basis of the Senis atlas # hs1 cross-links: hs1 varFreqs phasedVars Projects that provide haplotype-phased genotypes and variants hs1 phasedVars varFreqs Projects where variant frequencies, aka allele frequencies, are publicly available hs1 ~mappability problematic Regions that are hard to align to, and that often produce artifacts hs1 ~sedefSegDups censat Another class of highly repetitive sequence resolved by the T2T assembly hs1 ~simpleRepeat microsatellites Another annotation of short tandem repeats in the reference sequence # danRer11 cross-links: danRer11 >transMapV5 transMapV6 The current version of the TransMap alignments danRer11 ensGene refSeqComposite Gene models from NCBI RefSeq, curated independently of Ensembl danRer11 refSeqComposite ensGene Gene models from Ensembl, curated independently of RefSeq danRer11 ~simpleRepeat microsat Another annotation of short tandem repeats in the reference sequence +# Repeat annotation cross-links: +hg38 rmsk nestedRepeats Fragments of the same repeats joined by RepeatMasker ID, showing which pieces belong together +hg38 nestedRepeats rmsk The individual repeat annotations these fragments were joined from +hg38 rmsk joinedRmsk A detailed view of the same annotations, showing the alignment structure of each repeat +hg38 joinedRmsk rmsk The standard view of these annotations, one item per repeat +hg38 rmsk simpleRepeat Tandem repeats found by TRF, rather than the interspersed repeat families +hg38 simpleRepeat rmsk Interspersed repeats and low-complexity DNA, annotated by family +hg38 rmsk windowmaskerSdust An alternative masking of repetitive and low-complexity sequence, computed without a repeat library +hg38 windowmaskerSdust rmsk Repeats annotated by family from a curated library, rather than found de novo + +hg19 rmsk nestedRepeats Fragments of the same repeats joined by RepeatMasker ID, showing which pieces belong together +hg19 nestedRepeats rmsk The individual repeat annotations these fragments were joined from +hg19 rmsk simpleRepeat Tandem repeats found by TRF, rather than the interspersed repeat families +hg19 simpleRepeat rmsk Interspersed repeats and low-complexity DNA, annotated by family +hg19 rmsk windowmaskerSdust An alternative masking of repetitive and low-complexity sequence, computed without a repeat library +hg19 windowmaskerSdust rmsk Repeats annotated by family from a curated library, rather than found de novo + +mm39 rmsk nestedRepeats Fragments of the same repeats joined by RepeatMasker ID, showing which pieces belong together +mm39 nestedRepeats rmsk The individual repeat annotations these fragments were joined from +mm39 rmsk simpleRepeat Tandem repeats found by TRF, rather than the interspersed repeat families +mm39 simpleRepeat rmsk Interspersed repeats and low-complexity DNA, annotated by family +mm39 rmsk windowmaskerSdust An alternative masking of repetitive and low-complexity sequence, computed without a repeat library +mm39 windowmaskerSdust rmsk Repeats annotated by family from a curated library, rather than found de novo + +mm10 rmsk nestedRepeats Fragments of the same repeats joined by RepeatMasker ID, showing which pieces belong together +mm10 nestedRepeats rmsk The individual repeat annotations these fragments were joined from +mm10 rmsk joinedRmsk A detailed view of the same annotations, showing the alignment structure of each repeat +mm10 joinedRmsk rmsk The standard view of these annotations, one item per repeat +mm10 rmsk simpleRepeat Tandem repeats found by TRF, rather than the interspersed repeat families +mm10 simpleRepeat rmsk Interspersed repeats and low-complexity DNA, annotated by family +mm10 rmsk windowmaskerSdust An alternative masking of repetitive and low-complexity sequence, computed without a repeat library +mm10 windowmaskerSdust rmsk Repeats annotated by family from a curated library, rather than found de novo + +danRer11 rmsk nestedRepeats Fragments of the same repeats joined by RepeatMasker ID, showing which pieces belong together +danRer11 nestedRepeats rmsk The individual repeat annotations these fragments were joined from +danRer11 rmsk simpleRepeat Tandem repeats found by TRF, rather than the interspersed repeat families +danRer11 simpleRepeat rmsk Interspersed repeats and low-complexity DNA, annotated by family +danRer11 rmsk windowmaskerSdust An alternative masking of repetitive and low-complexity sequence, computed without a repeat library +danRer11 windowmaskerSdust rmsk Repeats annotated by family from a curated library, rather than found de novo + +# Literature and association cross-links: +hg38 gwasCatalog varsInPubs Individual variants mentioned in the literature, text-mined from full-text papers +hg38 varsInPubs gwasCatalog Trait and disease associations from published genome-wide association studies +hg38 gwasCatalog snpedia Wiki summaries of what has been published about individual SNPs +hg38 snpedia gwasCatalog The underlying published associations, with effect sizes and p-values +hg38 gwasCatalog gtexEqtlHighConf Variants that change gene expression, often used to find the gene behind an association signal +hg38 gtexEqtlHighConf gwasCatalog Trait and disease association signals these expression effects are usually compared against +hg38 snpedia varsInPubs Individual variants mentioned in the literature, text-mined from full-text papers +hg38 varsInPubs snpedia Wiki summaries of what has been published about individual SNPs + +hg19 gwasCatalog varsInPubs Individual variants mentioned in the literature, text-mined from full-text papers +hg19 varsInPubs gwasCatalog Trait and disease associations from published genome-wide association studies +hg19 gwasCatalog snpedia Wiki summaries of what has been published about individual SNPs +hg19 snpedia gwasCatalog The underlying published associations, with effect sizes and p-values +hg19 snpedia varsInPubs Individual variants mentioned in the literature, text-mined from full-text papers +hg19 varsInPubs snpedia Wiki summaries of what has been published about individual SNPs + # Variant impact predictor cross-links: hg38 mutScore primateAi A pathogenicity predictor that also works from 3D protein structure hg38 primateAi mutScore Missense variant clustering within 3D protein structures hg38 mutScore revel An ensemble missense pathogenicity score built from multiple predictors hg38 revel mutScore Missense variant clustering within 3D protein structures hg38 mutScore alphaMissense A deep-learning missense pathogenicity predictor hg38 alphaMissense mutScore Missense variant clustering within 3D protein structures hg38 mutScore clinPred An ensemble missense pathogenicity predictor that incorporates gnomAD allele frequency hg38 clinPred mutScore Missense variant clustering within 3D protein structures hg38 >caddSuper1_7 revel An ensemble pathogenicity score for coding variants hg38 >caddSuper1_7 clinPred An ensemble missense pathogenicity predictor that incorporates gnomAD allele frequency hg38 >caddSuper1_7 alphaMissense A deep-learning missense pathogenicity predictor hg38 >caddSuper1_7 gnomadVariants Population allele frequencies, useful for judging whether a high-scoring variant is common hg19 >caddSuper1_7 gnomadSuper Population allele frequencies, useful for judging whether a high-scoring variant is common