6796b337521a06767307b5c273bf89903d5a3bd6 lrnassar Tue Aug 11 17:05:08 2026 -0700 Fix Variant Evidence Summary SpliceAI/BP7 issues per code review. refs #37446 - Use the released spliceAIsnvsMasked.bb instead of a superseded symlink; the older /gbdb/hg38/bbi/spliceAi.bb pointed at a stale file the live track no longer serves. - Distinguish a SpliceAI lookup miss from a measured 0.00 in the mouseover. A miss now reads "no record (below the 0.02 reporting floor)"; BP7 still applies because the file's 0.02 floor means a missing score is below 0.1. - Correct the BP7 mouseover threshold text from "<= 0.1" to "< 0.1" to match the code, docstring, and makedoc. - Record PM1 suppression in the codeNotes field so it matches the autoSql description instead of leaving the field empty on every row. diff --git src/hg/makeDb/doc/Cardiomyopathy.txt src/hg/makeDb/doc/Cardiomyopathy.txt index 2fdcad99aa9..8bc89b17de8 100644 --- src/hg/makeDb/doc/Cardiomyopathy.txt +++ src/hg/makeDb/doc/Cardiomyopathy.txt @@ -187,32 +187,37 @@ # State at ClinVar release 2026-05-30: 199 records, 100% "reviewed by # expert panel". Classifications: 33 P + 32 LP + 75 VUS + 9 LB + 50 B = 199. # # # A.4 gnomAD v4.1 exomes (already on hgwdev; no download) # /hive/data/outside/gnomAD.4/v4.1/exomes/gnomad.exomes.v4.1.sites.chr{N}.vcf.bgz # Field used: fafmax_faf95_max (max FAF95 across genetic ancestry groups), # queried per-region via tabix. # Public mirror: https://hgdownload.soe.ucsc.edu/gbdb/hg38/gnomAD/v4.1/exomes/exomes.bb # # A.5 REVEL (already on hgwdev; no download) # /gbdb/hg38/revel/{a,c,g,t}.bw (per-alt-nucleotide bigwigs) # Public mirror: https://hgdownload.soe.ucsc.edu/gbdb/hg38/revel/ # # A.6 SpliceAI (already on hgwdev; no download) -# /gbdb/hg38/bbi/spliceAi.bb (bed9+4; AIscore in col 9, name="ref>alt") -# Used by the B.11 splice flag and BP7 (SpliceAI < 0.1). +# /gbdb/hg38/bbi/spliceAIsnvsMasked.bb (bed9+4; AIscore in col 9, name="ref>alt") +# This is the released masked-SNV file that the live UCSC spliceAI track serves. +# (The older /gbdb/hg38/bbi/spliceAi.bb symlink is superseded and no longer used.) +# Used by the B.11 splice flag and BP7 (SpliceAI < 0.1). The file has a 0.02 +# reporting floor, so a variant with no record has a true score below 0.02 +# (hence below 0.1): BP7 still applies, and the mouseover says "no record +# (below the 0.02 reporting floor)" rather than printing a default 0.00 as data. # # A.7 CardioBoost precomputed predictions # cmp_downloads/cardioboost/cm_prediction.RData (precomputed table, # ~65k rows; ~31k in our 8 genes — NOT just model objects) # Source: https://github.com/ImperialCardioGenetics/CardioBoost_manuscript # Loaded via /usr/bin/Rscript (the team Rscript is broken on hgwdev — # missing libgfortran.so.3). Coordinates are GRCh37 with numeric chrom # names; B.5 adds the chr prefix and liftOvers to hg38. # # A.8 Walsh PS4 + PM1 calibration supplements # mkdir -p cmp_downloads/walsh ; cd cmp_downloads/walsh # # Walsh 2017 (PS4 case-control) — Springer direct (avoids PMC PoW challenge) # curl -fsSL -o walsh2017_supplement.zip \ # "https://static-content.springer.com/esm/art%3A10.1038%2Fgim.2016.90/MediaObjects/41436_2017_BFgim201690_MOESM9_ESM.zip" # unzip -o walsh2017_supplement.zip # -> Supplementary_Tables_resubmit.xlsx @@ -362,31 +367,31 @@ # P/LP reference, leave-one-out; a variant cannot earn the code from its # own entry; PS1 reference excludes established splice-impact variants e.g. # MYBPC3 c.2308G>A), PM4 (NMD-escaping truncating, non-MYBPC3: last exon or # within 50 nt of the final exon-exon junction), BP7 (synonymous + # SpliceAI < 0.1, per Walker 2023 PMID 37352859; conservation requirement # removed per the VCEP). PM1<->PM5 mutual exclusion enforced per CSpec (keep # PM5, the variant-specific code; drop PM1; PM1+PS1 co-occurrence flagged). # HCM/DCM diseaseTag populated. A SpliceAI score >= 0.20 is recorded as an # informational splice flag. # Mouseover is evidence-first ("evidence -> supports CODE"); NO overall # classification is calculated. The GN002 combining logic remains in the # script as classify() but is retired/uncalled. Clinical/functional codes # (PS2/PS3/PS4/PP1/PP4/BS3/BS4) are not computed. Single neutral display # color 91,107,122; no classification encoded. # Output: 10,974 features. Evidence firing: BA1 210, BS1 367, PM2_Supporting -# 9,893, PP3 1,436, BP4 1,647, BP7 2,419, PM1 1,293, PM4 27, PM5 11, PS1 0. +# 9,893, PP3 1,436, BP4 1,647, BP7 2,415, PM1 1,293, PM4 27, PM5 11, PS1 0. ############################################################################## # Phase C: Hub assembly ############################################################################## # # Files written/maintained by hand (NOT generated by the build scripts): # hub.txt, genomes.txt # cardiomyopathy.html (shared description page; hub descriptionUrl) # hg38/trackDb.txt # hg19/trackDb.txt (mirrors hg38; differs in bigDataUrl + an hg19 # provenance header noting liftOver-derived coords) # # trackDb structure: 6 top-level groups -> 9 tracks. Two are composites: # Bioinformatic (REVEL on + CardioBoost off) and VCEP Curated Variants (EvRepo on