824df26b6320b692d629566c5a10b15004da82ce lrnassar Tue Sep 29 16:09:00 2026 -0700 addProteinSequence in mavemdLib translates each transcript's CDS from hg38.2bit so makeMaveMdVariants can check every projected codon against the reference residue its own HGVS term asserts; the existing comparison against MaveDB's genomic mapping only reaches the 3% of projected items that carry both terms, because 18 of the 40 protein accessions have no genomic-route variants at all. 39 of 40 accessions match at 0.000%; NP_689629.2 (FKRP) has 99 nonsense terms numbered one codon downstream of their own reference residue, which still reach mavemdVar through MaveDB's genomic mapping but are dropped from mavemdMap, which places columns from the protein term and has no fallback. The haplotype test now also reads hgvs_nt, since PTEN 00000054-a-1 states 1,236 haplotypes as c.[1207G>T;1209C>T] with no protein term and they were counted as rejected submissions, making both figures in the makeDoc wrong. assayLine runs the heatmap legend through asciiText because bedField turns the en dash in three MaveDB titles into – and the legend is drawn as raster text; clinGenId links to by_canonicalid rather than /allele, which serves JSON to a browser, matching human/civic.ra; the generated filter fragment no longer emits the blank line after each group that the makeDoc itself warns ends a stanza; and runBuild.sh tails the log on failure instead of dying silently under set -e. Also reworded the grey legend entry, which said no threshold was reached in either direction but covers 6,656 normal and 145 abnormal items, alphabetized the references, and fixed stale counts in the makeDoc. Caught by Claude review of 29af14b, fcf788d and 97c7de5. refs #38407 refs #37800 diff --git src/hg/makeDb/trackDb/human/hg38/mavemd.ra src/hg/makeDb/trackDb/human/hg38/mavemd.ra index 9952181eb34..bfbe5a3e39e 100644 --- src/hg/makeDb/trackDb/human/hg38/mavemd.ra +++ src/hg/makeDb/trackDb/human/hg38/mavemd.ra @@ -1,53 +1,53 @@ track mavemd superTrack on shortLabel MaveMD longLabel MaveMD: clinically calibrated multiplexed variant effect measurements group phenDis dataVersion /gbdb/$D/mavemd/version.txt track mavemdMap parent mavemd shortLabel MaveMD Maps longLabel MaveMD variant effect maps, colored by ACMG functional evidence type bigBed 12 + 20 bigDataUrl /gbdb/$D/mavemd/mavemdMap.bb style heatmap visibility pack priority 1 filterText.name .* filterType.name regexp filterLabel.name Gene or score set track mavemdVar parent mavemd shortLabel MaveMD Variants longLabel MaveMD individual variant measurements with ACMG functional evidence type bigBed 12 + 34 bigDataUrl /gbdb/$D/mavemd/mavemdVar.bb itemRgb on visibility dense priority 2 maxWindowCoverage 200000 searchIndex name,clinGenId,variantUrn skipEmptyFields on - urls publicationUrl="$$" scoreSet="https://mavedb.org/score-sets/$$" clinGenId="https://reg.clinicalgenome.org/allele/$$" + urls publicationUrl="$$" scoreSet="https://mavedb.org/score-sets/$$" clinGenId="https://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_canonicalid?canonicalid=$$" mouseOver <b>${name}</b><br><b>Effect:</b> ${funcClass}<br><b>Assay score:</b> ${funcScore}<br><b>Dataset:</b> ${scoreSetTitle}<br><b>ACMG evidence:</b> ${acmgOutcome} filterValues.acmgOutcome BS3,BS3_moderate,BS3_moderate_plus,BS3_supporting,BS3_very_strong,PS3,PS3_moderate,PS3_moderate_plus,PS3_not_met,PS3_supporting,PS3_very_strong filterLabel.acmgOutcome ACMG functional evidence filterValues.funcClass abnormal,indeterminate,normal filterLabel.funcClass Measured functional class filterValues.gene ASPA,BAP1,BARD1,BRCA1,BRCA2,CALM1,CARD11,CBS,CHEK2,CRX,CTCF,DDX3X,F9,FKRP,G6PD,GCK,HMBS,JAG1,KCNE1,KCNH2,KCNQ4,LARGE1,MSH2,NDUFAF6,OTC,PALB2,PAX6,PTEN,RAD51C,RAD51D,RHO,SCN5A,SGCB,TARDBP,TP53,TPK1,TSC2,VHL,XRCC2 filterLabel.gene Gene filterValues.clinvarSig Benign,Benign/Likely benign,Benign; association,Conflicting classifications of pathogenicity,Conflicting classifications of pathogenicity; other; risk factor,Conflicting classifications of pathogenicity; risk factor,Likely benign,Likely pathogenic,Likely pathogenic/Likely risk allele,Likely risk allele,Pathogenic,Pathogenic/Likely pathogenic,Pathogenic/Likely pathogenic/Likely risk allele,Pathogenic/Likely pathogenic/Pathogenic,, low penetrance,Uncertain risk allele,Uncertain significance,Uncertain significance/Uncertain risk allele,drug response,no classification for the single variant,not provided,other filterLabel.clinvarSig ClinVar significance filterValues.assayMethod Cell fitness,Cell morphology assay,Cell proliferation assay,Direct protein function,Flow cytometry assay,Not applicable (trained predictor),Reporter filterLabel.assayMethod Assay method filterValues.assayModel Immortalized human cells,Murine primary cells,Not applicable,Other,Yeast filterLabel.assayModel Assay model system filterValues.libraryMethod Endogenous locus library method,In vitro construct library method,N/A (meta-analysis) filterLabel.libraryMethod Variant library method searchTable mavemdVar searchType bigBed searchDescription MaveMD variant, ClinGen allele ID or MaveDB variant URN searchPriority 50