50466766840ded6cb8bd5cb868bdf2ff3f613bc0 lrnassar Tue Apr 21 11:17:15 2026 -0700 QA fixes for PrimateAI-3D track. Config (primateAi.ra): - Fix broken Ensembl transcript linkout: urls $S expanded to chromosome name; switch to the Ensembl transcript page with $$ - Add numeric filters on percentile and raw score (label notes the paper's 0.821 clinical threshold) - Add maxWindowToDraw 2000000 Data (primateAiToBigBed.py): - Change hardcoded strand '+' to '.': the source file has no strand column - Accept input/output paths as CLI args (previously hardcoded the hg38 input path) - Handle variable field count: ~2.4M rows in the hg19 source are missing the refseq column Description (primateAi.html): - Fix two broken hgTrackUi&... internal links to the Zoonomia 447-way track - Regenerate the first reference via getTrackReferences (wrong article number and wrong PMC ID in the previous text) - Fix the GitHub URL for the conversion script in Methods - Move the Zoonomia 447-way mention out of Description; rephrase the license note to describe precisely what is disabled relatedTracks.ra: - Add reciprocal cross-links for primateAi <-> alphaMissense (hg38), primateAi <-> revel (hg38 + hg19), and primateAi <-> promoterAi (hg38). Also includes promoterAi <-> alphaMissense cross-links. refs #37274 #37279 diff --git src/hg/makeDb/trackDb/relatedTracks.ra src/hg/makeDb/trackDb/relatedTracks.ra index 4930e91da8d..f0b122a368e 100644 --- src/hg/makeDb/trackDb/relatedTracks.ra +++ src/hg/makeDb/trackDb/relatedTracks.ra @@ -91,15 +91,30 @@ # mm10 ENCODE4 Regulation: mm10 encode4Reg encode3Reg Previous ENCODE3 Regulation track mm10 encode3Reg encode4Reg New ENCODE4 Regulation track mm10 encode4Reg cCREs Related ENCODE4 cCRE annotations mm10 cCREs encode4Reg Related ENCODE4 regulation data # hg38 long-read SV supertrack cross-links to other SV resources: hg38 lrSv gnomadStructuralVariants Short-read structural variants from gnomAD v4.1 hg38 gnomadStructuralVariants lrSv Long-read structural variants across multiple cohorts hg38 lrSv dbVarSv NCBI dbVar structural variants (short-read and long-read, germline and clinical) hg38 dbVarSv lrSv Long-read structural variants across multiple cohorts hg38 lrSv dgvPlus Database of Genomic Variants (DGV) structural variation catalog hg38 dgvPlus lrSv Long-read structural variants across multiple cohorts hg38 lrSv giabSv Genome in a Bottle high-confidence SV benchmark callsets hg38 giabSv lrSv Long-read structural variants across multiple cohorts + +# PrimateAI-3D cross-links: +hg38 primateAi alphaMissense AlphaMissense, a similar deep-learning missense pathogenicity predictor +hg38 alphaMissense primateAi PrimateAI-3D, a similar deep-learning missense pathogenicity predictor using primate variation +hg38 primateAi revel REVEL, an ensemble missense pathogenicity score built from multiple predictors +hg38 revel primateAi PrimateAI-3D, a missense pathogenicity predictor using primate variation and 3D protein structure + +hg19 primateAi revel REVEL, an ensemble missense pathogenicity score built from multiple predictors +hg19 revel primateAi PrimateAI-3D, a missense pathogenicity predictor using primate variation and 3D protein structure + +# PromoterAI cross-links: +hg38 promoterAi primateAi PrimateAI-3D, a companion deep-learning model from Illumina for coding (missense) variants +hg38 primateAi promoterAi PromoterAI, a companion deep-learning model from Illumina for non-coding promoter variants +hg38 promoterAi alphaMissense AlphaMissense, a deep-learning predictor of missense (coding) variant pathogenicity +hg38 alphaMissense promoterAi PromoterAI, a deep-learning predictor of expression-altering variants in promoter regions