File Changes for lrnassar

v498_preview2 to v498_base (2026-05-04 to 2026-05-11) v498

• src/hg/hgTracks/hgTracks.c
  • lines changed 1, context: html, text, full: html, text
    61117792d4e14c4f3daeb754964893f50592356d Wed May 6 19:10:46 2026 -0700
    Use Font Awesome info-circle for chromAlias icon and soften styling, refs #29201 Replace the unicode ⓘ (CIRCLED LATIN SMALL LETTER I) with the Font Awesome fa-info-circle icon to fix pixelated/inconsistent rendering in Chrome and Edge — the unicode glyph falls back to platform symbol fonts that produce low-quality bitmap glyphs at small sizes. The FA glyph is vector and renders identically across browsers. Also soften the icon color to #aaa, drop font-size to 95%, and tighten right margin to 0.1em.
• src/hg/htdocs/indexMeetings.html
  • lines changed 26, context: html, text, full: html, text
    c2e393e9426c225608ab90840d2c593f29a1a37f Thu May 7 12:22:25 2026 -0700
    Remove past HGM and CSHL meetings from indexMeetings page and rebalance columns. No RM.
• src/hg/htdocs/style/HGStyle.css
  • lines changed 3, context: html, text, full: html, text
    61117792d4e14c4f3daeb754964893f50592356d Wed May 6 19:10:46 2026 -0700
    Use Font Awesome info-circle for chromAlias icon and soften styling, refs #29201 Replace the unicode ⓘ (CIRCLED LATIN SMALL LETTER I) with the Font Awesome fa-info-circle icon to fix pixelated/inconsistent rendering in Chrome and Edge — the unicode glyph falls back to platform symbol fonts that produce low-quality bitmap glyphs at small sizes. The FA glyph is vector and renders identically across browsers. Also soften the icon color to #aaa, drop font-size to 95%, and tighten right margin to 0.1em.
• src/hg/makeDb/clinPred/clinPredToWig.py
  • lines changed 119, context: html, text, full: html, text
    f350ebff8f2cc1e0772032e59e926b5e45b374cd Tue May 5 16:18:28 2026 -0700
    Adding ClinPred missense pathogenicity score track on hg19 and hg38. refs #37510 ClinPred (Alirezaie et al, AJHG 2018) joins the predictionScoresSuper supertrack as a composite of four bigWigs, one per alternate base, with a per-position color overlay (red for score >= 0.5 likely pathogenic, blue for < 0.5 likely benign). Adds clinPredToWig.py to convert the upstream score table to wig, a clinPred branch in makeWigColorByRevelCadd.py for the color overlay step, and reciprocal relatedTracks entries to REVEL, CADD, PrimateAI-3D, and AlphaMissense. Also adds Display Conventions and Credits entries in predictionScoresSuper.html for ClinPred, PrimateAI-3D, and PromoterAI.
• src/hg/makeDb/doc/hg19.txt
  • lines changed 32, context: html, text, full: html, text
    f350ebff8f2cc1e0772032e59e926b5e45b374cd Tue May 5 16:18:28 2026 -0700
    Adding ClinPred missense pathogenicity score track on hg19 and hg38. refs #37510 ClinPred (Alirezaie et al, AJHG 2018) joins the predictionScoresSuper supertrack as a composite of four bigWigs, one per alternate base, with a per-position color overlay (red for score >= 0.5 likely pathogenic, blue for < 0.5 likely benign). Adds clinPredToWig.py to convert the upstream score table to wig, a clinPred branch in makeWigColorByRevelCadd.py for the color overlay step, and reciprocal relatedTracks entries to REVEL, CADD, PrimateAI-3D, and AlphaMissense. Also adds Display Conventions and Credits entries in predictionScoresSuper.html for ClinPred, PrimateAI-3D, and PromoterAI.
• src/hg/makeDb/doc/hg38/clinPred.txt
  • lines changed 29, context: html, text, full: html, text
    f350ebff8f2cc1e0772032e59e926b5e45b374cd Tue May 5 16:18:28 2026 -0700
    Adding ClinPred missense pathogenicity score track on hg19 and hg38. refs #37510 ClinPred (Alirezaie et al, AJHG 2018) joins the predictionScoresSuper supertrack as a composite of four bigWigs, one per alternate base, with a per-position color overlay (red for score >= 0.5 likely pathogenic, blue for < 0.5 likely benign). Adds clinPredToWig.py to convert the upstream score table to wig, a clinPred branch in makeWigColorByRevelCadd.py for the color overlay step, and reciprocal relatedTracks entries to REVEL, CADD, PrimateAI-3D, and AlphaMissense. Also adds Display Conventions and Credits entries in predictionScoresSuper.html for ClinPred, PrimateAI-3D, and PromoterAI.
• src/hg/makeDb/scripts/varFreqs/databases.tsv
  • lines changed 3, context: html, text, full: html, text
    ec5c73f4dc3ef4beae16fa1c12b7e5bf872bb73d Tue May 5 15:04:39 2026 -0700
    varFreqs: fix gaspIndel bigDataUrl after Max's GenomeAsia hg38 lift; add Tishkoff180 to combined-track filter UI; sync databases.tsv with deployed bigBed; minor description-page corrections. refs #36642 GenomeAsia hg38 lift (May 5 2026, by Max): - gaspIndel.bigDataUrl was pointing at the old GRCh37 filename "All.indels.annot.cont_withmaf.vcf.gz" which was renamed to "ga100k.indels.vcf.gz" during the lift; this left the gaspIndel track broken on the sandbox until the trackdb stanza was updated to match. - gasp/gaspIndel dataVersion strings updated from "Pilot 2019 (GRCh37 - to be lifted)" to "Pilot 2019 (lifted to hg38, May 2026)". - databases.tsv: also updated GenomeAsiaIndel path to ga100k.indels.vcf.gz so the next varFreqsAll rebuild reads from the lifted file. Tishkoff180 in varFreqsAll.bb but unfilterable (fresh-eyes audit finding): - Added Tishkoff180 to filterValues.sources and added filterByRange.Tishkoff180AF / Tishkoff180AC entries. - Added Tishkoff180 (and SVatalog) rows to databases.tsv to match the deployed bigBed (which already has those columns). Description-page corrections: - varFreqsAll.html: "20 population databases" -> "25 source databases" (matches actual count); HGDP+1kG bullet "European" -> "Non-Finnish European" to disambiguate from Finnish (gnomAD's nfe). - varFreqs.html: GenomeAsia row in the Available Datasets table updated from 3 to 7 sub-populations (NEA/SEA/SAS plus the previously hidden OCE/AMR/AFR/WER) so the table matches what the data exposes once Max's rebuild populates the new filter columns. - KOVA longLabel: "1.9k WGS+3.5k WES" -> "1.9k WGS+3.4k WES" (3.4k is correct per Lee 2017 and kova.html).
• src/hg/makeDb/scripts/varFreqs/populations.tsv
  • lines changed 6, context: html, text, full: html, text
    f674b74547b883a2054c4771533d753266e07c06 Mon May 4 16:21:54 2026 -0700
    QA pass on varFreqs supertrack: relabel HGDP+1kG and AllOfUs per-population fields to match data semantics, expose all 7 GenomeAsia populations in filter UI, normalize labels and capitalization, add Methods + References to description page, and flag GenomeAsia GRCh37 coordinate mismatch via dataVersion. refs #36642 trackDb (varFreqs.ra): - HGDP+1kG per-population AC/AF labels relabeled from "gnomAD HGDP+1kG <pop>" to "gnomAD v3.1.2 <pop> (full release)" since the values come from the full ~76k-genome gnomAD release, not the 4,094-genome HGDP+1kG cohort. - AllOfUs per-population AC/AF labels appended with "(local ancestry)" to clarify these are local-ancestry-stratified haplotype frequencies (Ioannidis lab pipeline), not the AllOfUs paper's global Rye categories. - Added 8 new filter entries for GenomeAsia OCE/AMR/AFR/WER (data has 7 population groups; trackUI previously exposed only 3). - shortLabel shortenings: alfaVcf, finngen, gasp, gaspIndel, kova, saudi, schema, colorsDbSnv, tishkoff180. - longLabel shortenings: ga4kSnv, colorsDbSnv, svatalogSnv, tishkoff180. - Capitalization fixes: SFARI Spark to SFARI SPARK, Japan ToMMO to Japan ToMMo, NHLBI TOPMED to NHLBI TOPMed. - dataVersion added on 6 subtracks that lacked it (gasp, gaspIndel, indigenomes, saudi, ga4kSnv, svatalogSnv); gasp/gaspIndel flagged "Pilot 2019 (GRCh37 - to be lifted)" for visibility of the open hg19 issue. - Default visibility flipped: non-summary subtracks now dense, summary varFreqsAll now pack. Container stays hide. Description page (varFreqs.html): - Added References section with 21 primary publications for the source cohorts. - Added "Notes on Specific Sub-tracks" explaining the HGDP+1kG cohort vs full-release distinction and the AllOfUs locAncFreq semantics. - Added Methods section describing per-subtrack and combined-track build pipelines, with links to the GitHub scripts directory and makedoc. - Encoded genome@soe.ucsc.edu with encodeEmail.pl. - Corrected "more than 1.2 billion variants" to "1.17 billion" (actual varFreqsAll.bb itemCount: 1,169,063,801). - Normalized body-text quotes to &quot; entities. - AllOfUs and HGDP+1kG rows in the datasets table now flag the semantic distinction inline. Build config (scripts/varFreqs/populations.tsv): - Added 4 GenomeAsia rows (OCE, AMR, AFR, WER) so the next varFreqsAll bigBed rebuild will populate the new filter columns. - Fixed HGDP1kG nfe label "European" to "Non-Finnish European" to match the trackdb relabel.
• src/hg/makeDb/scripts/wigColorByColors/makeWigColorByRevelCadd.py
  • lines changed 10, context: html, text, full: html, text
    f350ebff8f2cc1e0772032e59e926b5e45b374cd Tue May 5 16:18:28 2026 -0700
    Adding ClinPred missense pathogenicity score track on hg19 and hg38. refs #37510 ClinPred (Alirezaie et al, AJHG 2018) joins the predictionScoresSuper supertrack as a composite of four bigWigs, one per alternate base, with a per-position color overlay (red for score >= 0.5 likely pathogenic, blue for < 0.5 likely benign). Adds clinPredToWig.py to convert the upstream score table to wig, a clinPred branch in makeWigColorByRevelCadd.py for the color overlay step, and reciprocal relatedTracks entries to REVEL, CADD, PrimateAI-3D, and AlphaMissense. Also adds Display Conventions and Credits entries in predictionScoresSuper.html for ClinPred, PrimateAI-3D, and PromoterAI.
• src/hg/makeDb/trackDb/human/abraom.html
  • lines changed 1, context: html, text, full: html, text
    38bafc856320cf5360e0482faeee72b78f2ea963 Tue May 5 14:13:30 2026 -0700
    QA pass on varFreqs per-subtrack description pages: encode 3 plain emails, add target=_blank to 15 boilerplate REST API links, and add missing References sections (and Data Access on varFreqsAll). refs #36642 Mechanical fixes across 18 per-subtrack description pages: - Encoded 3 plain author/contact emails: pfeliciano@simonsfoundation.org (sfariSparkExomes), m.hobbs@garvan.org.au (mgrb), contact_npco@a-star.edu.sg (npm). - Added target="_blank" to 15 occurrences of the boilerplate "<a href=https://api.genome.ucsc.edu>REST API</a>" link across allofus, topmed, sfariSparkExomes, tommo60kjpn, alfaVcf, gasp, abraom, indigenomes, hrc, saudi, schema, sgdpFreq, gregor, hgdp1kFreq, colorsDbSnv. Added missing References sections: - allofus.html: All of Us Research Program 2024 Nature. - topmed.html: Taliun 2021 Nature. - alfaVcf.html: NCBI ALFA documentation citation (no peer-reviewed paper yet). - gregor.html: GREGoR R04 Methods document + consortium website (no flagship publication yet). - varFreqsAll.html: pointer to the supertrack's References section, plus tool citations (bcftools csq, Ensembl VEP). Added missing Data Access section on varFreqsAll.html explaining that the merged callset is not downloadable due to mixed source-data licensing, but can be reconstructed from the per-subtrack VCFs using the conversion scripts on GitHub. All 25 unique varFreqs description pages now have Description, Methods, Data Access, References. No non-ASCII characters and no inline event handlers across the set.
• src/hg/makeDb/trackDb/human/alfaVcf.html
  • lines changed 10, context: html, text, full: html, text
    38bafc856320cf5360e0482faeee72b78f2ea963 Tue May 5 14:13:30 2026 -0700
    QA pass on varFreqs per-subtrack description pages: encode 3 plain emails, add target=_blank to 15 boilerplate REST API links, and add missing References sections (and Data Access on varFreqsAll). refs #36642 Mechanical fixes across 18 per-subtrack description pages: - Encoded 3 plain author/contact emails: pfeliciano@simonsfoundation.org (sfariSparkExomes), m.hobbs@garvan.org.au (mgrb), contact_npco@a-star.edu.sg (npm). - Added target="_blank" to 15 occurrences of the boilerplate "<a href=https://api.genome.ucsc.edu>REST API</a>" link across allofus, topmed, sfariSparkExomes, tommo60kjpn, alfaVcf, gasp, abraom, indigenomes, hrc, saudi, schema, sgdpFreq, gregor, hgdp1kFreq, colorsDbSnv. Added missing References sections: - allofus.html: All of Us Research Program 2024 Nature. - topmed.html: Taliun 2021 Nature. - alfaVcf.html: NCBI ALFA documentation citation (no peer-reviewed paper yet). - gregor.html: GREGoR R04 Methods document + consortium website (no flagship publication yet). - varFreqsAll.html: pointer to the supertrack's References section, plus tool citations (bcftools csq, Ensembl VEP). Added missing Data Access section on varFreqsAll.html explaining that the merged callset is not downloadable due to mixed source-data licensing, but can be reconstructed from the per-subtrack VCFs using the conversion scripts on GitHub. All 25 unique varFreqs description pages now have Description, Methods, Data Access, References. No non-ASCII characters and no inline event handlers across the set.
  • lines changed 4, context: html, text, full: html, text
    c16022c991b55ffe9bb620746a6101346c920a67 Tue May 5 14:23:44 2026 -0700
    QA: claim cross-checks on varFreqs description pages; correct 1 internal contradiction and update 3 supertrack references to current/canonical papers. refs #36642 alfaVcf.html: the Description claimed "15.5 million rs sites" while the Methods (and the actual VCF, 163,487,286 records) reflected the post-conversion content. Updated the Description to "163 million variants (146 million SNPs and 17 million indels)" so Description and Methods now agree, and removed the outdated ClinVar count. varFreqs.html (supertrack References): - ABraOM: replaced Naslavsky 2017 Hum Mutat (the 609-individual exome paper) with Naslavsky 2022 Nat Commun (the 1,171-WGS paper), which is the flagship for the data we actually serve and is what abraom.html cites. - Mexico Biobank: added Sohail 2023 Nature ("Mexican Biobank advances population and medical genomics of diverse ancestries"), which is the descriptor paper for the 6,011-individual MEGA-array dataset; the supertrack page previously had no MexBB citation. - ToMMo: replaced Tadaka 2021 NAR (jMorp updates in 2020) with Tadaka 2024 NAR (jMorp Multi-Omics Reference Panel update report 2023), the more recent jMorp release note that tommo60kjpn.html already cites. Other claims spot-checked against the VCF and verified consistent: TopMed (header NS=150,899 matches the page; 868,581,653 records matches exactly), GenomeAsia (~65M / actual 66.2M; 1,739 individuals from 219 populations confirmed), GA4K (552 samples / AN=1,104 / 36.2M variants all verified), SVatalog (8.8M / actual 8,814,835), Tishkoff (33.6M / actual 33,600,472), Saudi (302 individuals / 25.5M variants).
• src/hg/makeDb/trackDb/human/allofus.html
  • lines changed 11, context: html, text, full: html, text
    38bafc856320cf5360e0482faeee72b78f2ea963 Tue May 5 14:13:30 2026 -0700
    QA pass on varFreqs per-subtrack description pages: encode 3 plain emails, add target=_blank to 15 boilerplate REST API links, and add missing References sections (and Data Access on varFreqsAll). refs #36642 Mechanical fixes across 18 per-subtrack description pages: - Encoded 3 plain author/contact emails: pfeliciano@simonsfoundation.org (sfariSparkExomes), m.hobbs@garvan.org.au (mgrb), contact_npco@a-star.edu.sg (npm). - Added target="_blank" to 15 occurrences of the boilerplate "<a href=https://api.genome.ucsc.edu>REST API</a>" link across allofus, topmed, sfariSparkExomes, tommo60kjpn, alfaVcf, gasp, abraom, indigenomes, hrc, saudi, schema, sgdpFreq, gregor, hgdp1kFreq, colorsDbSnv. Added missing References sections: - allofus.html: All of Us Research Program 2024 Nature. - topmed.html: Taliun 2021 Nature. - alfaVcf.html: NCBI ALFA documentation citation (no peer-reviewed paper yet). - gregor.html: GREGoR R04 Methods document + consortium website (no flagship publication yet). - varFreqsAll.html: pointer to the supertrack's References section, plus tool citations (bcftools csq, Ensembl VEP). Added missing Data Access section on varFreqsAll.html explaining that the merged callset is not downloadable due to mixed source-data licensing, but can be reconstructed from the per-subtrack VCFs using the conversion scripts on GitHub. All 25 unique varFreqs description pages now have Description, Methods, Data Access, References. No non-ASCII characters and no inline event handlers across the set.
• src/hg/makeDb/trackDb/human/clinPred.html
  • lines changed 126, context: html, text, full: html, text
    f350ebff8f2cc1e0772032e59e926b5e45b374cd Tue May 5 16:18:28 2026 -0700
    Adding ClinPred missense pathogenicity score track on hg19 and hg38. refs #37510 ClinPred (Alirezaie et al, AJHG 2018) joins the predictionScoresSuper supertrack as a composite of four bigWigs, one per alternate base, with a per-position color overlay (red for score >= 0.5 likely pathogenic, blue for < 0.5 likely benign). Adds clinPredToWig.py to convert the upstream score table to wig, a clinPred branch in makeWigColorByRevelCadd.py for the color overlay step, and reciprocal relatedTracks entries to REVEL, CADD, PrimateAI-3D, and AlphaMissense. Also adds Display Conventions and Credits entries in predictionScoresSuper.html for ClinPred, PrimateAI-3D, and PromoterAI.
• src/hg/makeDb/trackDb/human/clinPred.ra
  • lines changed 70, context: html, text, full: html, text
    f350ebff8f2cc1e0772032e59e926b5e45b374cd Tue May 5 16:18:28 2026 -0700
    Adding ClinPred missense pathogenicity score track on hg19 and hg38. refs #37510 ClinPred (Alirezaie et al, AJHG 2018) joins the predictionScoresSuper supertrack as a composite of four bigWigs, one per alternate base, with a per-position color overlay (red for score >= 0.5 likely pathogenic, blue for < 0.5 likely benign). Adds clinPredToWig.py to convert the upstream score table to wig, a clinPred branch in makeWigColorByRevelCadd.py for the color overlay step, and reciprocal relatedTracks entries to REVEL, CADD, PrimateAI-3D, and AlphaMissense. Also adds Display Conventions and Credits entries in predictionScoresSuper.html for ClinPred, PrimateAI-3D, and PromoterAI.
• src/hg/makeDb/trackDb/human/colorsDbSnv.html
  • lines changed 1, context: html, text, full: html, text
    38bafc856320cf5360e0482faeee72b78f2ea963 Tue May 5 14:13:30 2026 -0700
    QA pass on varFreqs per-subtrack description pages: encode 3 plain emails, add target=_blank to 15 boilerplate REST API links, and add missing References sections (and Data Access on varFreqsAll). refs #36642 Mechanical fixes across 18 per-subtrack description pages: - Encoded 3 plain author/contact emails: pfeliciano@simonsfoundation.org (sfariSparkExomes), m.hobbs@garvan.org.au (mgrb), contact_npco@a-star.edu.sg (npm). - Added target="_blank" to 15 occurrences of the boilerplate "<a href=https://api.genome.ucsc.edu>REST API</a>" link across allofus, topmed, sfariSparkExomes, tommo60kjpn, alfaVcf, gasp, abraom, indigenomes, hrc, saudi, schema, sgdpFreq, gregor, hgdp1kFreq, colorsDbSnv. Added missing References sections: - allofus.html: All of Us Research Program 2024 Nature. - topmed.html: Taliun 2021 Nature. - alfaVcf.html: NCBI ALFA documentation citation (no peer-reviewed paper yet). - gregor.html: GREGoR R04 Methods document + consortium website (no flagship publication yet). - varFreqsAll.html: pointer to the supertrack's References section, plus tool citations (bcftools csq, Ensembl VEP). Added missing Data Access section on varFreqsAll.html explaining that the merged callset is not downloadable due to mixed source-data licensing, but can be reconstructed from the per-subtrack VCFs using the conversion scripts on GitHub. All 25 unique varFreqs description pages now have Description, Methods, Data Access, References. No non-ASCII characters and no inline event handlers across the set.
• src/hg/makeDb/trackDb/human/gasp.html
  • lines changed 1, context: html, text, full: html, text
    38bafc856320cf5360e0482faeee72b78f2ea963 Tue May 5 14:13:30 2026 -0700
    QA pass on varFreqs per-subtrack description pages: encode 3 plain emails, add target=_blank to 15 boilerplate REST API links, and add missing References sections (and Data Access on varFreqsAll). refs #36642 Mechanical fixes across 18 per-subtrack description pages: - Encoded 3 plain author/contact emails: pfeliciano@simonsfoundation.org (sfariSparkExomes), m.hobbs@garvan.org.au (mgrb), contact_npco@a-star.edu.sg (npm). - Added target="_blank" to 15 occurrences of the boilerplate "<a href=https://api.genome.ucsc.edu>REST API</a>" link across allofus, topmed, sfariSparkExomes, tommo60kjpn, alfaVcf, gasp, abraom, indigenomes, hrc, saudi, schema, sgdpFreq, gregor, hgdp1kFreq, colorsDbSnv. Added missing References sections: - allofus.html: All of Us Research Program 2024 Nature. - topmed.html: Taliun 2021 Nature. - alfaVcf.html: NCBI ALFA documentation citation (no peer-reviewed paper yet). - gregor.html: GREGoR R04 Methods document + consortium website (no flagship publication yet). - varFreqsAll.html: pointer to the supertrack's References section, plus tool citations (bcftools csq, Ensembl VEP). Added missing Data Access section on varFreqsAll.html explaining that the merged callset is not downloadable due to mixed source-data licensing, but can be reconstructed from the per-subtrack VCFs using the conversion scripts on GitHub. All 25 unique varFreqs description pages now have Description, Methods, Data Access, References. No non-ASCII characters and no inline event handlers across the set.
• src/hg/makeDb/trackDb/human/gregor.html
  • lines changed 10, context: html, text, full: html, text
    38bafc856320cf5360e0482faeee72b78f2ea963 Tue May 5 14:13:30 2026 -0700
    QA pass on varFreqs per-subtrack description pages: encode 3 plain emails, add target=_blank to 15 boilerplate REST API links, and add missing References sections (and Data Access on varFreqsAll). refs #36642 Mechanical fixes across 18 per-subtrack description pages: - Encoded 3 plain author/contact emails: pfeliciano@simonsfoundation.org (sfariSparkExomes), m.hobbs@garvan.org.au (mgrb), contact_npco@a-star.edu.sg (npm). - Added target="_blank" to 15 occurrences of the boilerplate "<a href=https://api.genome.ucsc.edu>REST API</a>" link across allofus, topmed, sfariSparkExomes, tommo60kjpn, alfaVcf, gasp, abraom, indigenomes, hrc, saudi, schema, sgdpFreq, gregor, hgdp1kFreq, colorsDbSnv. Added missing References sections: - allofus.html: All of Us Research Program 2024 Nature. - topmed.html: Taliun 2021 Nature. - alfaVcf.html: NCBI ALFA documentation citation (no peer-reviewed paper yet). - gregor.html: GREGoR R04 Methods document + consortium website (no flagship publication yet). - varFreqsAll.html: pointer to the supertrack's References section, plus tool citations (bcftools csq, Ensembl VEP). Added missing Data Access section on varFreqsAll.html explaining that the merged callset is not downloadable due to mixed source-data licensing, but can be reconstructed from the per-subtrack VCFs using the conversion scripts on GitHub. All 25 unique varFreqs description pages now have Description, Methods, Data Access, References. No non-ASCII characters and no inline event handlers across the set.
• src/hg/makeDb/trackDb/human/hg38/mpraVarDb.html
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    5d554d5ba53a383b1805bd4d3958a3aa2dce1cbb Tue May 5 14:33:19 2026 -0700
    Replace &nbsp; with regular spaces in mpraVarDb.html per CR feedback. refs #37504
• src/hg/makeDb/trackDb/human/hgdp1kFreq.html
  • lines changed 1, context: html, text, full: html, text
    38bafc856320cf5360e0482faeee72b78f2ea963 Tue May 5 14:13:30 2026 -0700
    QA pass on varFreqs per-subtrack description pages: encode 3 plain emails, add target=_blank to 15 boilerplate REST API links, and add missing References sections (and Data Access on varFreqsAll). refs #36642 Mechanical fixes across 18 per-subtrack description pages: - Encoded 3 plain author/contact emails: pfeliciano@simonsfoundation.org (sfariSparkExomes), m.hobbs@garvan.org.au (mgrb), contact_npco@a-star.edu.sg (npm). - Added target="_blank" to 15 occurrences of the boilerplate "<a href=https://api.genome.ucsc.edu>REST API</a>" link across allofus, topmed, sfariSparkExomes, tommo60kjpn, alfaVcf, gasp, abraom, indigenomes, hrc, saudi, schema, sgdpFreq, gregor, hgdp1kFreq, colorsDbSnv. Added missing References sections: - allofus.html: All of Us Research Program 2024 Nature. - topmed.html: Taliun 2021 Nature. - alfaVcf.html: NCBI ALFA documentation citation (no peer-reviewed paper yet). - gregor.html: GREGoR R04 Methods document + consortium website (no flagship publication yet). - varFreqsAll.html: pointer to the supertrack's References section, plus tool citations (bcftools csq, Ensembl VEP). Added missing Data Access section on varFreqsAll.html explaining that the merged callset is not downloadable due to mixed source-data licensing, but can be reconstructed from the per-subtrack VCFs using the conversion scripts on GitHub. All 25 unique varFreqs description pages now have Description, Methods, Data Access, References. No non-ASCII characters and no inline event handlers across the set.
• src/hg/makeDb/trackDb/human/hrc.html
  • lines changed 1, context: html, text, full: html, text
    38bafc856320cf5360e0482faeee72b78f2ea963 Tue May 5 14:13:30 2026 -0700
    QA pass on varFreqs per-subtrack description pages: encode 3 plain emails, add target=_blank to 15 boilerplate REST API links, and add missing References sections (and Data Access on varFreqsAll). refs #36642 Mechanical fixes across 18 per-subtrack description pages: - Encoded 3 plain author/contact emails: pfeliciano@simonsfoundation.org (sfariSparkExomes), m.hobbs@garvan.org.au (mgrb), contact_npco@a-star.edu.sg (npm). - Added target="_blank" to 15 occurrences of the boilerplate "<a href=https://api.genome.ucsc.edu>REST API</a>" link across allofus, topmed, sfariSparkExomes, tommo60kjpn, alfaVcf, gasp, abraom, indigenomes, hrc, saudi, schema, sgdpFreq, gregor, hgdp1kFreq, colorsDbSnv. Added missing References sections: - allofus.html: All of Us Research Program 2024 Nature. - topmed.html: Taliun 2021 Nature. - alfaVcf.html: NCBI ALFA documentation citation (no peer-reviewed paper yet). - gregor.html: GREGoR R04 Methods document + consortium website (no flagship publication yet). - varFreqsAll.html: pointer to the supertrack's References section, plus tool citations (bcftools csq, Ensembl VEP). Added missing Data Access section on varFreqsAll.html explaining that the merged callset is not downloadable due to mixed source-data licensing, but can be reconstructed from the per-subtrack VCFs using the conversion scripts on GitHub. All 25 unique varFreqs description pages now have Description, Methods, Data Access, References. No non-ASCII characters and no inline event handlers across the set.
• src/hg/makeDb/trackDb/human/indigenomes.html
  • lines changed 1, context: html, text, full: html, text
    38bafc856320cf5360e0482faeee72b78f2ea963 Tue May 5 14:13:30 2026 -0700
    QA pass on varFreqs per-subtrack description pages: encode 3 plain emails, add target=_blank to 15 boilerplate REST API links, and add missing References sections (and Data Access on varFreqsAll). refs #36642 Mechanical fixes across 18 per-subtrack description pages: - Encoded 3 plain author/contact emails: pfeliciano@simonsfoundation.org (sfariSparkExomes), m.hobbs@garvan.org.au (mgrb), contact_npco@a-star.edu.sg (npm). - Added target="_blank" to 15 occurrences of the boilerplate "<a href=https://api.genome.ucsc.edu>REST API</a>" link across allofus, topmed, sfariSparkExomes, tommo60kjpn, alfaVcf, gasp, abraom, indigenomes, hrc, saudi, schema, sgdpFreq, gregor, hgdp1kFreq, colorsDbSnv. Added missing References sections: - allofus.html: All of Us Research Program 2024 Nature. - topmed.html: Taliun 2021 Nature. - alfaVcf.html: NCBI ALFA documentation citation (no peer-reviewed paper yet). - gregor.html: GREGoR R04 Methods document + consortium website (no flagship publication yet). - varFreqsAll.html: pointer to the supertrack's References section, plus tool citations (bcftools csq, Ensembl VEP). Added missing Data Access section on varFreqsAll.html explaining that the merged callset is not downloadable due to mixed source-data licensing, but can be reconstructed from the per-subtrack VCFs using the conversion scripts on GitHub. All 25 unique varFreqs description pages now have Description, Methods, Data Access, References. No non-ASCII characters and no inline event handlers across the set.
• src/hg/makeDb/trackDb/human/mgrb.html
  • lines changed 1, context: html, text, full: html, text
    38bafc856320cf5360e0482faeee72b78f2ea963 Tue May 5 14:13:30 2026 -0700
    QA pass on varFreqs per-subtrack description pages: encode 3 plain emails, add target=_blank to 15 boilerplate REST API links, and add missing References sections (and Data Access on varFreqsAll). refs #36642 Mechanical fixes across 18 per-subtrack description pages: - Encoded 3 plain author/contact emails: pfeliciano@simonsfoundation.org (sfariSparkExomes), m.hobbs@garvan.org.au (mgrb), contact_npco@a-star.edu.sg (npm). - Added target="_blank" to 15 occurrences of the boilerplate "<a href=https://api.genome.ucsc.edu>REST API</a>" link across allofus, topmed, sfariSparkExomes, tommo60kjpn, alfaVcf, gasp, abraom, indigenomes, hrc, saudi, schema, sgdpFreq, gregor, hgdp1kFreq, colorsDbSnv. Added missing References sections: - allofus.html: All of Us Research Program 2024 Nature. - topmed.html: Taliun 2021 Nature. - alfaVcf.html: NCBI ALFA documentation citation (no peer-reviewed paper yet). - gregor.html: GREGoR R04 Methods document + consortium website (no flagship publication yet). - varFreqsAll.html: pointer to the supertrack's References section, plus tool citations (bcftools csq, Ensembl VEP). Added missing Data Access section on varFreqsAll.html explaining that the merged callset is not downloadable due to mixed source-data licensing, but can be reconstructed from the per-subtrack VCFs using the conversion scripts on GitHub. All 25 unique varFreqs description pages now have Description, Methods, Data Access, References. No non-ASCII characters and no inline event handlers across the set.
• src/hg/makeDb/trackDb/human/npm.html
  • lines changed 1, context: html, text, full: html, text
    38bafc856320cf5360e0482faeee72b78f2ea963 Tue May 5 14:13:30 2026 -0700
    QA pass on varFreqs per-subtrack description pages: encode 3 plain emails, add target=_blank to 15 boilerplate REST API links, and add missing References sections (and Data Access on varFreqsAll). refs #36642 Mechanical fixes across 18 per-subtrack description pages: - Encoded 3 plain author/contact emails: pfeliciano@simonsfoundation.org (sfariSparkExomes), m.hobbs@garvan.org.au (mgrb), contact_npco@a-star.edu.sg (npm). - Added target="_blank" to 15 occurrences of the boilerplate "<a href=https://api.genome.ucsc.edu>REST API</a>" link across allofus, topmed, sfariSparkExomes, tommo60kjpn, alfaVcf, gasp, abraom, indigenomes, hrc, saudi, schema, sgdpFreq, gregor, hgdp1kFreq, colorsDbSnv. Added missing References sections: - allofus.html: All of Us Research Program 2024 Nature. - topmed.html: Taliun 2021 Nature. - alfaVcf.html: NCBI ALFA documentation citation (no peer-reviewed paper yet). - gregor.html: GREGoR R04 Methods document + consortium website (no flagship publication yet). - varFreqsAll.html: pointer to the supertrack's References section, plus tool citations (bcftools csq, Ensembl VEP). Added missing Data Access section on varFreqsAll.html explaining that the merged callset is not downloadable due to mixed source-data licensing, but can be reconstructed from the per-subtrack VCFs using the conversion scripts on GitHub. All 25 unique varFreqs description pages now have Description, Methods, Data Access, References. No non-ASCII characters and no inline event handlers across the set.
• src/hg/makeDb/trackDb/human/predictionScoresSuper.html
  • lines changed 47, context: html, text, full: html, text
    f350ebff8f2cc1e0772032e59e926b5e45b374cd Tue May 5 16:18:28 2026 -0700
    Adding ClinPred missense pathogenicity score track on hg19 and hg38. refs #37510 ClinPred (Alirezaie et al, AJHG 2018) joins the predictionScoresSuper supertrack as a composite of four bigWigs, one per alternate base, with a per-position color overlay (red for score >= 0.5 likely pathogenic, blue for < 0.5 likely benign). Adds clinPredToWig.py to convert the upstream score table to wig, a clinPred branch in makeWigColorByRevelCadd.py for the color overlay step, and reciprocal relatedTracks entries to REVEL, CADD, PrimateAI-3D, and AlphaMissense. Also adds Display Conventions and Credits entries in predictionScoresSuper.html for ClinPred, PrimateAI-3D, and PromoterAI.
• src/hg/makeDb/trackDb/human/predictionScoresSuper.ra
  • lines changed 1, context: html, text, full: html, text
    f350ebff8f2cc1e0772032e59e926b5e45b374cd Tue May 5 16:18:28 2026 -0700
    Adding ClinPred missense pathogenicity score track on hg19 and hg38. refs #37510 ClinPred (Alirezaie et al, AJHG 2018) joins the predictionScoresSuper supertrack as a composite of four bigWigs, one per alternate base, with a per-position color overlay (red for score >= 0.5 likely pathogenic, blue for < 0.5 likely benign). Adds clinPredToWig.py to convert the upstream score table to wig, a clinPred branch in makeWigColorByRevelCadd.py for the color overlay step, and reciprocal relatedTracks entries to REVEL, CADD, PrimateAI-3D, and AlphaMissense. Also adds Display Conventions and Credits entries in predictionScoresSuper.html for ClinPred, PrimateAI-3D, and PromoterAI.
• src/hg/makeDb/trackDb/human/saudi.html
  • lines changed 1, context: html, text, full: html, text
    38bafc856320cf5360e0482faeee72b78f2ea963 Tue May 5 14:13:30 2026 -0700
    QA pass on varFreqs per-subtrack description pages: encode 3 plain emails, add target=_blank to 15 boilerplate REST API links, and add missing References sections (and Data Access on varFreqsAll). refs #36642 Mechanical fixes across 18 per-subtrack description pages: - Encoded 3 plain author/contact emails: pfeliciano@simonsfoundation.org (sfariSparkExomes), m.hobbs@garvan.org.au (mgrb), contact_npco@a-star.edu.sg (npm). - Added target="_blank" to 15 occurrences of the boilerplate "<a href=https://api.genome.ucsc.edu>REST API</a>" link across allofus, topmed, sfariSparkExomes, tommo60kjpn, alfaVcf, gasp, abraom, indigenomes, hrc, saudi, schema, sgdpFreq, gregor, hgdp1kFreq, colorsDbSnv. Added missing References sections: - allofus.html: All of Us Research Program 2024 Nature. - topmed.html: Taliun 2021 Nature. - alfaVcf.html: NCBI ALFA documentation citation (no peer-reviewed paper yet). - gregor.html: GREGoR R04 Methods document + consortium website (no flagship publication yet). - varFreqsAll.html: pointer to the supertrack's References section, plus tool citations (bcftools csq, Ensembl VEP). Added missing Data Access section on varFreqsAll.html explaining that the merged callset is not downloadable due to mixed source-data licensing, but can be reconstructed from the per-subtrack VCFs using the conversion scripts on GitHub. All 25 unique varFreqs description pages now have Description, Methods, Data Access, References. No non-ASCII characters and no inline event handlers across the set.
• src/hg/makeDb/trackDb/human/schema.html
  • lines changed 1, context: html, text, full: html, text
    38bafc856320cf5360e0482faeee72b78f2ea963 Tue May 5 14:13:30 2026 -0700
    QA pass on varFreqs per-subtrack description pages: encode 3 plain emails, add target=_blank to 15 boilerplate REST API links, and add missing References sections (and Data Access on varFreqsAll). refs #36642 Mechanical fixes across 18 per-subtrack description pages: - Encoded 3 plain author/contact emails: pfeliciano@simonsfoundation.org (sfariSparkExomes), m.hobbs@garvan.org.au (mgrb), contact_npco@a-star.edu.sg (npm). - Added target="_blank" to 15 occurrences of the boilerplate "<a href=https://api.genome.ucsc.edu>REST API</a>" link across allofus, topmed, sfariSparkExomes, tommo60kjpn, alfaVcf, gasp, abraom, indigenomes, hrc, saudi, schema, sgdpFreq, gregor, hgdp1kFreq, colorsDbSnv. Added missing References sections: - allofus.html: All of Us Research Program 2024 Nature. - topmed.html: Taliun 2021 Nature. - alfaVcf.html: NCBI ALFA documentation citation (no peer-reviewed paper yet). - gregor.html: GREGoR R04 Methods document + consortium website (no flagship publication yet). - varFreqsAll.html: pointer to the supertrack's References section, plus tool citations (bcftools csq, Ensembl VEP). Added missing Data Access section on varFreqsAll.html explaining that the merged callset is not downloadable due to mixed source-data licensing, but can be reconstructed from the per-subtrack VCFs using the conversion scripts on GitHub. All 25 unique varFreqs description pages now have Description, Methods, Data Access, References. No non-ASCII characters and no inline event handlers across the set.
• src/hg/makeDb/trackDb/human/sfariSparkExomes.html
  • lines changed 2, context: html, text, full: html, text
    38bafc856320cf5360e0482faeee72b78f2ea963 Tue May 5 14:13:30 2026 -0700
    QA pass on varFreqs per-subtrack description pages: encode 3 plain emails, add target=_blank to 15 boilerplate REST API links, and add missing References sections (and Data Access on varFreqsAll). refs #36642 Mechanical fixes across 18 per-subtrack description pages: - Encoded 3 plain author/contact emails: pfeliciano@simonsfoundation.org (sfariSparkExomes), m.hobbs@garvan.org.au (mgrb), contact_npco@a-star.edu.sg (npm). - Added target="_blank" to 15 occurrences of the boilerplate "<a href=https://api.genome.ucsc.edu>REST API</a>" link across allofus, topmed, sfariSparkExomes, tommo60kjpn, alfaVcf, gasp, abraom, indigenomes, hrc, saudi, schema, sgdpFreq, gregor, hgdp1kFreq, colorsDbSnv. Added missing References sections: - allofus.html: All of Us Research Program 2024 Nature. - topmed.html: Taliun 2021 Nature. - alfaVcf.html: NCBI ALFA documentation citation (no peer-reviewed paper yet). - gregor.html: GREGoR R04 Methods document + consortium website (no flagship publication yet). - varFreqsAll.html: pointer to the supertrack's References section, plus tool citations (bcftools csq, Ensembl VEP). Added missing Data Access section on varFreqsAll.html explaining that the merged callset is not downloadable due to mixed source-data licensing, but can be reconstructed from the per-subtrack VCFs using the conversion scripts on GitHub. All 25 unique varFreqs description pages now have Description, Methods, Data Access, References. No non-ASCII characters and no inline event handlers across the set.
• src/hg/makeDb/trackDb/human/sgdpFreq.html
  • lines changed 1, context: html, text, full: html, text
    38bafc856320cf5360e0482faeee72b78f2ea963 Tue May 5 14:13:30 2026 -0700
    QA pass on varFreqs per-subtrack description pages: encode 3 plain emails, add target=_blank to 15 boilerplate REST API links, and add missing References sections (and Data Access on varFreqsAll). refs #36642 Mechanical fixes across 18 per-subtrack description pages: - Encoded 3 plain author/contact emails: pfeliciano@simonsfoundation.org (sfariSparkExomes), m.hobbs@garvan.org.au (mgrb), contact_npco@a-star.edu.sg (npm). - Added target="_blank" to 15 occurrences of the boilerplate "<a href=https://api.genome.ucsc.edu>REST API</a>" link across allofus, topmed, sfariSparkExomes, tommo60kjpn, alfaVcf, gasp, abraom, indigenomes, hrc, saudi, schema, sgdpFreq, gregor, hgdp1kFreq, colorsDbSnv. Added missing References sections: - allofus.html: All of Us Research Program 2024 Nature. - topmed.html: Taliun 2021 Nature. - alfaVcf.html: NCBI ALFA documentation citation (no peer-reviewed paper yet). - gregor.html: GREGoR R04 Methods document + consortium website (no flagship publication yet). - varFreqsAll.html: pointer to the supertrack's References section, plus tool citations (bcftools csq, Ensembl VEP). Added missing Data Access section on varFreqsAll.html explaining that the merged callset is not downloadable due to mixed source-data licensing, but can be reconstructed from the per-subtrack VCFs using the conversion scripts on GitHub. All 25 unique varFreqs description pages now have Description, Methods, Data Access, References. No non-ASCII characters and no inline event handlers across the set.
• src/hg/makeDb/trackDb/human/tommo60kjpn.html
  • lines changed 1, context: html, text, full: html, text
    38bafc856320cf5360e0482faeee72b78f2ea963 Tue May 5 14:13:30 2026 -0700
    QA pass on varFreqs per-subtrack description pages: encode 3 plain emails, add target=_blank to 15 boilerplate REST API links, and add missing References sections (and Data Access on varFreqsAll). refs #36642 Mechanical fixes across 18 per-subtrack description pages: - Encoded 3 plain author/contact emails: pfeliciano@simonsfoundation.org (sfariSparkExomes), m.hobbs@garvan.org.au (mgrb), contact_npco@a-star.edu.sg (npm). - Added target="_blank" to 15 occurrences of the boilerplate "<a href=https://api.genome.ucsc.edu>REST API</a>" link across allofus, topmed, sfariSparkExomes, tommo60kjpn, alfaVcf, gasp, abraom, indigenomes, hrc, saudi, schema, sgdpFreq, gregor, hgdp1kFreq, colorsDbSnv. Added missing References sections: - allofus.html: All of Us Research Program 2024 Nature. - topmed.html: Taliun 2021 Nature. - alfaVcf.html: NCBI ALFA documentation citation (no peer-reviewed paper yet). - gregor.html: GREGoR R04 Methods document + consortium website (no flagship publication yet). - varFreqsAll.html: pointer to the supertrack's References section, plus tool citations (bcftools csq, Ensembl VEP). Added missing Data Access section on varFreqsAll.html explaining that the merged callset is not downloadable due to mixed source-data licensing, but can be reconstructed from the per-subtrack VCFs using the conversion scripts on GitHub. All 25 unique varFreqs description pages now have Description, Methods, Data Access, References. No non-ASCII characters and no inline event handlers across the set.
• src/hg/makeDb/trackDb/human/topmed.html
  • lines changed 12, context: html, text, full: html, text
    38bafc856320cf5360e0482faeee72b78f2ea963 Tue May 5 14:13:30 2026 -0700
    QA pass on varFreqs per-subtrack description pages: encode 3 plain emails, add target=_blank to 15 boilerplate REST API links, and add missing References sections (and Data Access on varFreqsAll). refs #36642 Mechanical fixes across 18 per-subtrack description pages: - Encoded 3 plain author/contact emails: pfeliciano@simonsfoundation.org (sfariSparkExomes), m.hobbs@garvan.org.au (mgrb), contact_npco@a-star.edu.sg (npm). - Added target="_blank" to 15 occurrences of the boilerplate "<a href=https://api.genome.ucsc.edu>REST API</a>" link across allofus, topmed, sfariSparkExomes, tommo60kjpn, alfaVcf, gasp, abraom, indigenomes, hrc, saudi, schema, sgdpFreq, gregor, hgdp1kFreq, colorsDbSnv. Added missing References sections: - allofus.html: All of Us Research Program 2024 Nature. - topmed.html: Taliun 2021 Nature. - alfaVcf.html: NCBI ALFA documentation citation (no peer-reviewed paper yet). - gregor.html: GREGoR R04 Methods document + consortium website (no flagship publication yet). - varFreqsAll.html: pointer to the supertrack's References section, plus tool citations (bcftools csq, Ensembl VEP). Added missing Data Access section on varFreqsAll.html explaining that the merged callset is not downloadable due to mixed source-data licensing, but can be reconstructed from the per-subtrack VCFs using the conversion scripts on GitHub. All 25 unique varFreqs description pages now have Description, Methods, Data Access, References. No non-ASCII characters and no inline event handlers across the set.
• src/hg/makeDb/trackDb/human/varFreqs.html
  • lines changed 282, context: html, text, full: html, text
    f674b74547b883a2054c4771533d753266e07c06 Mon May 4 16:21:54 2026 -0700
    QA pass on varFreqs supertrack: relabel HGDP+1kG and AllOfUs per-population fields to match data semantics, expose all 7 GenomeAsia populations in filter UI, normalize labels and capitalization, add Methods + References to description page, and flag GenomeAsia GRCh37 coordinate mismatch via dataVersion. refs #36642 trackDb (varFreqs.ra): - HGDP+1kG per-population AC/AF labels relabeled from "gnomAD HGDP+1kG <pop>" to "gnomAD v3.1.2 <pop> (full release)" since the values come from the full ~76k-genome gnomAD release, not the 4,094-genome HGDP+1kG cohort. - AllOfUs per-population AC/AF labels appended with "(local ancestry)" to clarify these are local-ancestry-stratified haplotype frequencies (Ioannidis lab pipeline), not the AllOfUs paper's global Rye categories. - Added 8 new filter entries for GenomeAsia OCE/AMR/AFR/WER (data has 7 population groups; trackUI previously exposed only 3). - shortLabel shortenings: alfaVcf, finngen, gasp, gaspIndel, kova, saudi, schema, colorsDbSnv, tishkoff180. - longLabel shortenings: ga4kSnv, colorsDbSnv, svatalogSnv, tishkoff180. - Capitalization fixes: SFARI Spark to SFARI SPARK, Japan ToMMO to Japan ToMMo, NHLBI TOPMED to NHLBI TOPMed. - dataVersion added on 6 subtracks that lacked it (gasp, gaspIndel, indigenomes, saudi, ga4kSnv, svatalogSnv); gasp/gaspIndel flagged "Pilot 2019 (GRCh37 - to be lifted)" for visibility of the open hg19 issue. - Default visibility flipped: non-summary subtracks now dense, summary varFreqsAll now pack. Container stays hide. Description page (varFreqs.html): - Added References section with 21 primary publications for the source cohorts. - Added "Notes on Specific Sub-tracks" explaining the HGDP+1kG cohort vs full-release distinction and the AllOfUs locAncFreq semantics. - Added Methods section describing per-subtrack and combined-track build pipelines, with links to the GitHub scripts directory and makedoc. - Encoded genome@soe.ucsc.edu with encodeEmail.pl. - Corrected "more than 1.2 billion variants" to "1.17 billion" (actual varFreqsAll.bb itemCount: 1,169,063,801). - Normalized body-text quotes to &quot; entities. - AllOfUs and HGDP+1kG rows in the datasets table now flag the semantic distinction inline. Build config (scripts/varFreqs/populations.tsv): - Added 4 GenomeAsia rows (OCE, AMR, AFR, WER) so the next varFreqsAll bigBed rebuild will populate the new filter columns. - Fixed HGDP1kG nfe label "European" to "Non-Finnish European" to match the trackdb relabel.
  • lines changed 26, context: html, text, full: html, text
    c16022c991b55ffe9bb620746a6101346c920a67 Tue May 5 14:23:44 2026 -0700
    QA: claim cross-checks on varFreqs description pages; correct 1 internal contradiction and update 3 supertrack references to current/canonical papers. refs #36642 alfaVcf.html: the Description claimed "15.5 million rs sites" while the Methods (and the actual VCF, 163,487,286 records) reflected the post-conversion content. Updated the Description to "163 million variants (146 million SNPs and 17 million indels)" so Description and Methods now agree, and removed the outdated ClinVar count. varFreqs.html (supertrack References): - ABraOM: replaced Naslavsky 2017 Hum Mutat (the 609-individual exome paper) with Naslavsky 2022 Nat Commun (the 1,171-WGS paper), which is the flagship for the data we actually serve and is what abraom.html cites. - Mexico Biobank: added Sohail 2023 Nature ("Mexican Biobank advances population and medical genomics of diverse ancestries"), which is the descriptor paper for the 6,011-individual MEGA-array dataset; the supertrack page previously had no MexBB citation. - ToMMo: replaced Tadaka 2021 NAR (jMorp updates in 2020) with Tadaka 2024 NAR (jMorp Multi-Omics Reference Panel update report 2023), the more recent jMorp release note that tommo60kjpn.html already cites. Other claims spot-checked against the VCF and verified consistent: TopMed (header NS=150,899 matches the page; 868,581,653 records matches exactly), GenomeAsia (~65M / actual 66.2M; 1,739 individuals from 219 populations confirmed), GA4K (552 samples / AN=1,104 / 36.2M variants all verified), SVatalog (8.8M / actual 8,814,835), Tishkoff (33.6M / actual 33,600,472), Saudi (302 individuals / 25.5M variants).
  • lines changed 2, context: html, text, full: html, text
    ec5c73f4dc3ef4beae16fa1c12b7e5bf872bb73d Tue May 5 15:04:39 2026 -0700
    varFreqs: fix gaspIndel bigDataUrl after Max's GenomeAsia hg38 lift; add Tishkoff180 to combined-track filter UI; sync databases.tsv with deployed bigBed; minor description-page corrections. refs #36642 GenomeAsia hg38 lift (May 5 2026, by Max): - gaspIndel.bigDataUrl was pointing at the old GRCh37 filename "All.indels.annot.cont_withmaf.vcf.gz" which was renamed to "ga100k.indels.vcf.gz" during the lift; this left the gaspIndel track broken on the sandbox until the trackdb stanza was updated to match. - gasp/gaspIndel dataVersion strings updated from "Pilot 2019 (GRCh37 - to be lifted)" to "Pilot 2019 (lifted to hg38, May 2026)". - databases.tsv: also updated GenomeAsiaIndel path to ga100k.indels.vcf.gz so the next varFreqsAll rebuild reads from the lifted file. Tishkoff180 in varFreqsAll.bb but unfilterable (fresh-eyes audit finding): - Added Tishkoff180 to filterValues.sources and added filterByRange.Tishkoff180AF / Tishkoff180AC entries. - Added Tishkoff180 (and SVatalog) rows to databases.tsv to match the deployed bigBed (which already has those columns). Description-page corrections: - varFreqsAll.html: "20 population databases" -> "25 source databases" (matches actual count); HGDP+1kG bullet "European" -> "Non-Finnish European" to disambiguate from Finnish (gnomAD's nfe). - varFreqs.html: GenomeAsia row in the Available Datasets table updated from 3 to 7 sub-populations (NEA/SEA/SAS plus the previously hidden OCE/AMR/AFR/WER) so the table matches what the data exposes once Max's rebuild populates the new filter columns. - KOVA longLabel: "1.9k WGS+3.5k WES" -> "1.9k WGS+3.4k WES" (3.4k is correct per Lee 2017 and kova.html).
• src/hg/makeDb/trackDb/human/varFreqs.ra
  • lines changed 110, context: html, text, full: html, text
    f674b74547b883a2054c4771533d753266e07c06 Mon May 4 16:21:54 2026 -0700
    QA pass on varFreqs supertrack: relabel HGDP+1kG and AllOfUs per-population fields to match data semantics, expose all 7 GenomeAsia populations in filter UI, normalize labels and capitalization, add Methods + References to description page, and flag GenomeAsia GRCh37 coordinate mismatch via dataVersion. refs #36642 trackDb (varFreqs.ra): - HGDP+1kG per-population AC/AF labels relabeled from "gnomAD HGDP+1kG <pop>" to "gnomAD v3.1.2 <pop> (full release)" since the values come from the full ~76k-genome gnomAD release, not the 4,094-genome HGDP+1kG cohort. - AllOfUs per-population AC/AF labels appended with "(local ancestry)" to clarify these are local-ancestry-stratified haplotype frequencies (Ioannidis lab pipeline), not the AllOfUs paper's global Rye categories. - Added 8 new filter entries for GenomeAsia OCE/AMR/AFR/WER (data has 7 population groups; trackUI previously exposed only 3). - shortLabel shortenings: alfaVcf, finngen, gasp, gaspIndel, kova, saudi, schema, colorsDbSnv, tishkoff180. - longLabel shortenings: ga4kSnv, colorsDbSnv, svatalogSnv, tishkoff180. - Capitalization fixes: SFARI Spark to SFARI SPARK, Japan ToMMO to Japan ToMMo, NHLBI TOPMED to NHLBI TOPMed. - dataVersion added on 6 subtracks that lacked it (gasp, gaspIndel, indigenomes, saudi, ga4kSnv, svatalogSnv); gasp/gaspIndel flagged "Pilot 2019 (GRCh37 - to be lifted)" for visibility of the open hg19 issue. - Default visibility flipped: non-summary subtracks now dense, summary varFreqsAll now pack. Container stays hide. Description page (varFreqs.html): - Added References section with 21 primary publications for the source cohorts. - Added "Notes on Specific Sub-tracks" explaining the HGDP+1kG cohort vs full-release distinction and the AllOfUs locAncFreq semantics. - Added Methods section describing per-subtrack and combined-track build pipelines, with links to the GitHub scripts directory and makedoc. - Encoded genome@soe.ucsc.edu with encodeEmail.pl. - Corrected "more than 1.2 billion variants" to "1.17 billion" (actual varFreqsAll.bb itemCount: 1,169,063,801). - Normalized body-text quotes to &quot; entities. - AllOfUs and HGDP+1kG rows in the datasets table now flag the semantic distinction inline. Build config (scripts/varFreqs/populations.tsv): - Added 4 GenomeAsia rows (OCE, AMR, AFR, WER) so the next varFreqsAll bigBed rebuild will populate the new filter columns. - Fixed HGDP1kG nfe label "European" to "Non-Finnish European" to match the trackdb relabel.
  • lines changed 9, context: html, text, full: html, text
    ec5c73f4dc3ef4beae16fa1c12b7e5bf872bb73d Tue May 5 15:04:39 2026 -0700
    varFreqs: fix gaspIndel bigDataUrl after Max's GenomeAsia hg38 lift; add Tishkoff180 to combined-track filter UI; sync databases.tsv with deployed bigBed; minor description-page corrections. refs #36642 GenomeAsia hg38 lift (May 5 2026, by Max): - gaspIndel.bigDataUrl was pointing at the old GRCh37 filename "All.indels.annot.cont_withmaf.vcf.gz" which was renamed to "ga100k.indels.vcf.gz" during the lift; this left the gaspIndel track broken on the sandbox until the trackdb stanza was updated to match. - gasp/gaspIndel dataVersion strings updated from "Pilot 2019 (GRCh37 - to be lifted)" to "Pilot 2019 (lifted to hg38, May 2026)". - databases.tsv: also updated GenomeAsiaIndel path to ga100k.indels.vcf.gz so the next varFreqsAll rebuild reads from the lifted file. Tishkoff180 in varFreqsAll.bb but unfilterable (fresh-eyes audit finding): - Added Tishkoff180 to filterValues.sources and added filterByRange.Tishkoff180AF / Tishkoff180AC entries. - Added Tishkoff180 (and SVatalog) rows to databases.tsv to match the deployed bigBed (which already has those columns). Description-page corrections: - varFreqsAll.html: "20 population databases" -> "25 source databases" (matches actual count); HGDP+1kG bullet "European" -> "Non-Finnish European" to disambiguate from Finnish (gnomAD's nfe). - varFreqs.html: GenomeAsia row in the Available Datasets table updated from 3 to 7 sub-populations (NEA/SEA/SAS plus the previously hidden OCE/AMR/AFR/WER) so the table matches what the data exposes once Max's rebuild populates the new filter columns. - KOVA longLabel: "1.9k WGS+3.5k WES" -> "1.9k WGS+3.4k WES" (3.4k is correct per Lee 2017 and kova.html).
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    8790628157f14caae701bfc3d793150127c13812 Tue May 5 16:27:53 2026 -0700
    varFreqs: add a 7-line mouseOver to the varFreqsAll combined track exposing variant identity, AA change, var type, consequence, max AF, total AC, and source databases. refs #36642 Replaces a previously commented-out 2-field mouseOver with a labeled 7-line tooltip designed to answer the questions a user typically has on hover: what is this variant, what protein change does it cause, which consequence bucket, how rare is it, how many alleles, and which population databases call it. The fields are the existing AutoSql columns on varFreqsAll.bb so no data rebuild is required.
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    dfee6d0940b88f5e537a436263bcb7f8bea5d3a8 Tue May 5 16:42:04 2026 -0700
    varFreqs: fix varFreqsAll mouseOver to use HTML (<br> + <b>) instead of \n. refs #36642 The previous commit 8790628157f used \n for line breaks, which is not what UCSC trackdb mouseOver supports — the trackDb tooltip renders the value as HTML, so newlines need to be <br> tags. Verified live in the sandbox: data-tooltip on each <area> now correctly renders with bolded labels and line breaks. Also bolds the field labels (Var, AA change, Var type, Conseq, Max AF, Total AC, Sources) for readability, matching the convention seen in uniprot.ra and other tracks.
• src/hg/makeDb/trackDb/human/varFreqsAll.html
  • lines changed 43, context: html, text, full: html, text
    38bafc856320cf5360e0482faeee72b78f2ea963 Tue May 5 14:13:30 2026 -0700
    QA pass on varFreqs per-subtrack description pages: encode 3 plain emails, add target=_blank to 15 boilerplate REST API links, and add missing References sections (and Data Access on varFreqsAll). refs #36642 Mechanical fixes across 18 per-subtrack description pages: - Encoded 3 plain author/contact emails: pfeliciano@simonsfoundation.org (sfariSparkExomes), m.hobbs@garvan.org.au (mgrb), contact_npco@a-star.edu.sg (npm). - Added target="_blank" to 15 occurrences of the boilerplate "<a href=https://api.genome.ucsc.edu>REST API</a>" link across allofus, topmed, sfariSparkExomes, tommo60kjpn, alfaVcf, gasp, abraom, indigenomes, hrc, saudi, schema, sgdpFreq, gregor, hgdp1kFreq, colorsDbSnv. Added missing References sections: - allofus.html: All of Us Research Program 2024 Nature. - topmed.html: Taliun 2021 Nature. - alfaVcf.html: NCBI ALFA documentation citation (no peer-reviewed paper yet). - gregor.html: GREGoR R04 Methods document + consortium website (no flagship publication yet). - varFreqsAll.html: pointer to the supertrack's References section, plus tool citations (bcftools csq, Ensembl VEP). Added missing Data Access section on varFreqsAll.html explaining that the merged callset is not downloadable due to mixed source-data licensing, but can be reconstructed from the per-subtrack VCFs using the conversion scripts on GitHub. All 25 unique varFreqs description pages now have Description, Methods, Data Access, References. No non-ASCII characters and no inline event handlers across the set.
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    ec5c73f4dc3ef4beae16fa1c12b7e5bf872bb73d Tue May 5 15:04:39 2026 -0700
    varFreqs: fix gaspIndel bigDataUrl after Max's GenomeAsia hg38 lift; add Tishkoff180 to combined-track filter UI; sync databases.tsv with deployed bigBed; minor description-page corrections. refs #36642 GenomeAsia hg38 lift (May 5 2026, by Max): - gaspIndel.bigDataUrl was pointing at the old GRCh37 filename "All.indels.annot.cont_withmaf.vcf.gz" which was renamed to "ga100k.indels.vcf.gz" during the lift; this left the gaspIndel track broken on the sandbox until the trackdb stanza was updated to match. - gasp/gaspIndel dataVersion strings updated from "Pilot 2019 (GRCh37 - to be lifted)" to "Pilot 2019 (lifted to hg38, May 2026)". - databases.tsv: also updated GenomeAsiaIndel path to ga100k.indels.vcf.gz so the next varFreqsAll rebuild reads from the lifted file. Tishkoff180 in varFreqsAll.bb but unfilterable (fresh-eyes audit finding): - Added Tishkoff180 to filterValues.sources and added filterByRange.Tishkoff180AF / Tishkoff180AC entries. - Added Tishkoff180 (and SVatalog) rows to databases.tsv to match the deployed bigBed (which already has those columns). Description-page corrections: - varFreqsAll.html: "20 population databases" -> "25 source databases" (matches actual count); HGDP+1kG bullet "European" -> "Non-Finnish European" to disambiguate from Finnish (gnomAD's nfe). - varFreqs.html: GenomeAsia row in the Available Datasets table updated from 3 to 7 sub-populations (NEA/SEA/SAS plus the previously hidden OCE/AMR/AFR/WER) so the table matches what the data exposes once Max's rebuild populates the new filter columns. - KOVA longLabel: "1.9k WGS+3.5k WES" -> "1.9k WGS+3.4k WES" (3.4k is correct per Lee 2017 and kova.html).
• src/hg/makeDb/trackDb/relatedTracks.ra
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    f350ebff8f2cc1e0772032e59e926b5e45b374cd Tue May 5 16:18:28 2026 -0700
    Adding ClinPred missense pathogenicity score track on hg19 and hg38. refs #37510 ClinPred (Alirezaie et al, AJHG 2018) joins the predictionScoresSuper supertrack as a composite of four bigWigs, one per alternate base, with a per-position color overlay (red for score >= 0.5 likely pathogenic, blue for < 0.5 likely benign). Adds clinPredToWig.py to convert the upstream score table to wig, a clinPred branch in makeWigColorByRevelCadd.py for the color overlay step, and reciprocal relatedTracks entries to REVEL, CADD, PrimateAI-3D, and AlphaMissense. Also adds Display Conventions and Credits entries in predictionScoresSuper.html for ClinPred, PrimateAI-3D, and PromoterAI.
• src/hg/utils/rts/rtsUpdate
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    1b38723574b05053668a698a9856652a077fce2f Mon May 4 14:48:55 2026 -0700
    First draft of rtsUpdate, a utility to streamline pushing Recommended Track Set sessions from a curator session through dev -> beta -> RR. Replaces the manual download-and-resave-on-every-mirror process. Each step is gated by an interactive confirmation; RR push has an additional --i-confirm-rr flag and a 5-second pause. Cart contents written via MySQL _binary 0xHEX literals for binary safety; sessionName regex-validated; WHERE clauses are exact-equality only. The kent tree (rts/<db>/<sessionName>) is the canonical backup, tracked by git. Not yet exercised against a live update. refs #32768