527a3531a7db419bad01537556693e9424e0ee04 max Fri Sep 8 05:00:23 2023 -0700 removing the trackDb prefix for clinvar tracks, no redmine diff --git src/hg/makeDb/trackDb/human/trackDb.clinvar.ra src/hg/makeDb/trackDb/human/trackDb.clinvar.ra deleted file mode 100644 index 01f4966..0000000 --- src/hg/makeDb/trackDb/human/trackDb.clinvar.ra +++ /dev/null @@ -1,105 +0,0 @@ -track clinvar -compositeTrack on -shortLabel ClinVar Variants -longLabel ClinVar Variants -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) - - track clinvarMain - parent clinvar - shortLabel ClinVar SNVs - longLabel ClinVar Short 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 - mouseOverField _mouseOver - bigDataUrl /gbdb/$D/bbi/clinvar/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 - - track clinvarCnv - parent clinvar - shortLabel ClinVar CNVs - longLabel ClinVar 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/clinvar/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/$$/" - noScoreFilter on - searchIndex _dbVarSsvId - - track clinvarSubLolly - parent clinvar - shortLabel ClinVar interp - longLabel ClinVar SNVs submitted interpretations and evidence - bigDataUrl /gbdb/$D/clinvarSubLolly/clinvarSubLolly.bb - xrefDataUrl /gbdb/$D/clinvarSubLolly/clinvarSub.bb - type bigLolly - group phenDis - lollySizeField 10 - yAxisNumLabels off - lollyNoStems on - configurable off - skipFields reviewStatus - yAxisLabel.0 0 on 150,150,150 OTH - yAxisLabel.1 1 on 150,150,150 B - yAxisLabel.2 2 on 150,150,150 LB - yAxisLabel.3 3 on 150,150,150 VUS - yAxisLabel.4 4 on 150,150,150 LP - yAxisLabel.5 5 on 150,150,150 P - lollyMaxSize 10 - viewLimits 0:5 - mouseOverField _mouseOver - urls rcvAcc="https://www.ncbi.nlm.nih.gov/clinvar/$$/" 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/$$/" origName="https://www.ncbi.nlm.nih.gov/clinvar/variation/$$/" - -searchTable clinvarCnv -searchType bigBed -searchDescription ClinVar Copy Number Variants -termRegex ^[ne]ssv[0-9]+ - -searchTable clinvarMain -searchType bigBed -searchDescription ClinVar Copy Number Variants -termRegex ^[ne]ssv[0-9]+