e68cc6315fa92edde16a3e27015a15cb94290440 jnavarr5 Thu May 22 14:34:00 2025 -0700 Adding files that were staged as the otto user, no Redmine. diff --git src/hg/makeDb/trackDb/human/clinvar.alpha.ra src/hg/makeDb/trackDb/human/clinvar.alpha.ra index a06f50c1147..b6678f4863c 100644 --- src/hg/makeDb/trackDb/human/clinvar.alpha.ra +++ src/hg/makeDb/trackDb/human/clinvar.alpha.ra @@ -1,93 +1,92 @@ track clinvarAlpha compositeTrack on shortLabel ClinVar Variants ALPHA longLabel ClinVar Variants ALPHA group phenDis visibility hide type bed 12 + noParentConfig on itemRgb on urls rcvAcc="https://www.ncbi.nlm.nih.gov/clinvar/$$/" geneId="https://www.ncbi.nlm.nih.gov/gene/$$" snpId="https://www.ncbi.nlm.nih.gov/snp/$$" nsvId="https://www.ncbi.nlm.nih.gov/dbvar/variants/$$/" origName="https://www.ncbi.nlm.nih.gov/clinvar/variation/$$/" scoreLabel ClinVar Star-Rating (0-4) dataVersion /gbdb/$D/bbi/clinvarAlpha/version.txt track clinvarMainAlpha parent clinvarAlpha - shortLabel ClinVar SNVs - longLabel ClinVar Short Variants < 50bp + shortLabel ClinVar SNVs ALPHA + longLabel ClinVar ALPHA Short Nucleotide Variants < 50bp visibility hide group phenDis itemRgb on priority 1 type bigBed 12 + showCfg on # note that you cannot change these values. Old carts will contain them. If you must change these, you'll have to rename # the field, which will reset the cart variables. Or use the cart rewrite mechanism. You can add more values, though filterValues._clinSignCode BN|benign,LB|likely benign,CF|conflicting,PG|pathogenic,LP|likely pathogenic,RF|risk factor,OT|other,VUS|vus filterType._clinSignCode multiple filterValues._originCode GERM|germline,SOM|somatic,GERMSOM|germline/somatic,UNK|unknown filterType._originCode multiple filterLabel._originCode Alelle Origin filterValues._allTypeCode SUBST|single nucleotide variant - SUBST,STRUCT|translocation and fusion - STRUCT,LOSS|deletion and copy loss - LOSS,GAIN|duplication and copy gain - GAIN,INS|indel and insertion - INS,INV|inversion - INV,SEQALT|undetermined - SEQALT,SEQLEN|repeat change - SEQLEN filterType._allTypeCode multiple filter._varLen 0 skipFields rcvAcc filterByRange._varLen on filterLimits._varLen 0:49 filterValues.molConseq genic downstream transcript variant|genic downstream transcript variant,no sequence alteration|no sequence alteration,inframe indel|inframe indel,stop lost|stop lost,genic upstream transcript variant|genic upstream transcript variant,initiatior codon variant|initiatior codon variant,inframe insertion|inframe insertion,inframe deletion|inframe deletion,splice acceptor variant|splice acceptor variant,splice donor variant|splice donor variant,5 prime UTR variant|5 prime UTR variant,nonsense|nonsense,non-coding transcript variant|non-coding transcript variant,3 prime UTR variant|3 prime UTR variant,frameshift variant|frameshift variant,intron variant|intron variant,synonymous variant|synonymous variant,missense variant|missense variant,|unknown,initiator codon variant|initiator codon variant mouseOverField _mouseOver bigDataUrl /gbdb/$D/bbi/clinvarAlpha/clinvarMain.bb urls rcvAcc="https://www.ncbi.nlm.nih.gov/clinvar/$$/" geneId="https://www.ncbi.nlm.nih.gov/gene/$$" snpId="https://www.ncbi.nlm.nih.gov/snp/$$" nsvId="https://www.ncbi.nlm.nih.gov/dbvar/variants/$$/" origName="https://www.ncbi.nlm.nih.gov/clinvar/variation/$$/" noScoreFilter on searchIndex _dbVarSsvId maxWindowCoverage 10000000 - decorator.default.bigDataUrl /gbdb/$D/bbi/clinvarAlpha/clinvarMainDecor.bb track clinvarCnvAlpha parent clinvarAlpha - shortLabel ClinVar CNVs - longLabel ClinVar Copy Number Variants >= 50bp + shortLabel ClinVar CNVs ALPHA + longLabel ClinVar ALPHA Copy Number Variants >= 50bp visibility hide type bigBed 12 + itemRgb on group phenDis priority 2 skipFields rcvAcc # note that you cannot change these values. Old carts will contain them. If you must change these, you'll have to rename # the field, which will reset the cart variables. Or use the cart rewrite mechanism. You can add more values, though filterValues._originCode GERM|germline,SOM|somatic,GERMSOM|germline/somatic,NOVO|de novo,UNK|unknown filterType._originCode multiple filterLabel._originCode Alelle Origin filterValues._allTypeCode SUBST|single nucleotide variant - SUBST,STRUCT|translocation and fusion - STRUCT,LOSS|deletion and copy loss - LOSS,GAIN|duplication and copy gain - GAIN,INS|indel and insertion - INS,INV|inversion - INV,SEQALT|undetermined - SEQALT,SEQLEN|repeat change - SEQLEN filterType._allTypeCode multiple filterValues._clinSignCode BN|benign,LB|likely benign,CF|conflicting,PG|pathogenic,LP|likely pathogenic,UC|uncertain,OT|other filterType._clinSignCode multiple filter._varLen 50:999999999 filterByRange._varLen on filterLimits._varLen 50:999999999 mouseOverField _mouseOver bigDataUrl /gbdb/$D/bbi/clinvarAlpha/clinvarCnv.bb mergeSpannedItems on urls rcvAcc="https://www.ncbi.nlm.nih.gov/clinvar/$$/" geneId="https://www.ncbi.nlm.nih.gov/gene/$$" snpId="https://www.ncbi.nlm.nih.gov/snp/$$" nsvId="https://www.ncbi.nlm.nih.gov/dbvar/variants/$$/" origName="https://www.ncbi.nlm.nih.gov/clinvar/variation/$$/" noScoreFilter on searchIndex _dbVarSsvId track clinvarSubLollyAlpha parent clinvarAlpha - shortLabel ClinVar interp - longLabel ClinVar SNVs submitted interpretations and evidence + shortLabel ClinVar interp ALPHA + longLabel ClinVar SNVs ALPHA submitted interpretations and evidence bigDataUrl /gbdb/$D/clinvarSubLollyAlpha/clinvarSubLolly.bb xrefDataUrl /gbdb/$D/clinvarSubLollyAlph/clinvarSub.bb type bigLolly group phenDis lollySizeField 10 yAxisNumLabels off lollyNoStems on configurable off skipFields reviewStatus yAxisLabel.0 0 on 150,150,150 OTH yAxisLabel.1 1 on 150,150,150 B yAxisLabel.2 2 on 150,150,150 LB yAxisLabel.3 3 on 150,150,150 VUS yAxisLabel.4 4 on 150,150,150 LP yAxisLabel.5 5 on 150,150,150 P