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/clinvar.ra src/hg/makeDb/trackDb/human/clinvar.ra new file mode 100644 index 0000000..01f4966 --- /dev/null +++ src/hg/makeDb/trackDb/human/clinvar.ra @@ -0,0 +1,105 @@ +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]+