f350ebff8f2cc1e0772032e59e926b5e45b374cd
lrnassar
  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.

diff --git src/hg/makeDb/trackDb/relatedTracks.ra src/hg/makeDb/trackDb/relatedTracks.ra
index 43a221ddb1f..2d717891115 100644
--- src/hg/makeDb/trackDb/relatedTracks.ra
+++ src/hg/makeDb/trackDb/relatedTracks.ra
@@ -101,30 +101,49 @@
 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
 
+# ClinPred cross-links:
+hg38 clinPred revel REVEL, an ensemble missense pathogenicity score using a similar machine-learning approach
+hg38 revel clinPred ClinPred, an ensemble missense pathogenicity predictor that incorporates gnomAD allele frequency
+hg38 clinPred caddSuper CADD, a similar deleteriousness score
+hg38 caddSuper clinPred ClinPred, a missense-only pathogenicity predictor
+hg38 clinPred primateAi PrimateAI-3D, a missense pathogenicity predictor using primate variation
+hg38 primateAi clinPred ClinPred, an ensemble missense predictor incorporating gnomAD allele frequency
+hg38 clinPred alphaMissense AlphaMissense, a deep-learning missense pathogenicity predictor
+hg38 alphaMissense clinPred ClinPred, an ensemble missense predictor incorporating gnomAD allele frequency
+
+hg19 clinPred revel REVEL, an ensemble missense pathogenicity score using a similar machine-learning approach
+hg19 revel clinPred ClinPred, an ensemble missense pathogenicity predictor that incorporates gnomAD allele frequency
+hg19 clinPred caddSuper CADD, a similar deleteriousness score
+hg19 caddSuper clinPred ClinPred, a missense-only pathogenicity predictor
+hg19 clinPred primateAi PrimateAI-3D, a missense pathogenicity predictor using primate variation
+hg19 primateAi clinPred ClinPred, an ensemble missense predictor incorporating gnomAD allele frequency
+hg19 clinPred alphaMissense AlphaMissense, a deep-learning missense pathogenicity predictor
+hg19 alphaMissense clinPred ClinPred, an ensemble missense predictor incorporating gnomAD allele frequency
+
 # 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
 
 # NMD Escape cross-links:
 hg38 nmd mane MANE Select transcripts from NCBI/EBI, a curated subset of RefSeq/Ensembl transcripts used as clinical reference
 hg38 mane nmd NMD Escape: predicted regions where premature termination codons escape nonsense-mediated decay
 hg38 nmd ncbiRefSeq NCBI RefSeq transcripts, the source annotation set for the NMD Escape RefSeq subtrack
 hg38 ncbiRefSeq nmd NMD Escape: predicted regions where premature termination codons escape nonsense-mediated decay
 
 # MPRA cross-links:
 hg38 mpra wgEncodeReg4 ENCODE regulatory region annotations, many of which are tested by MPRA assays
 hg38 wgEncodeReg4 mpra Experimental MPRA measurements of regulatory activity for candidate elements