8e1de594b0f580652a3a7b4f1d1a3865356077fc lrnassar Fri Sep 11 11:47:29 2020 -0700 Removing test.ra for clinVar track improvements refs #24850 diff --git src/hg/makeDb/trackDb/human/trackDb.clinvar.ra src/hg/makeDb/trackDb/human/trackDb.clinvar.ra index c4be9d9..14cac1c 100644 --- src/hg/makeDb/trackDb/human/trackDb.clinvar.ra +++ src/hg/makeDb/trackDb/human/trackDb.clinvar.ra @@ -1,30 +1,72 @@ 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/projects/SNP/snp_ref.cgi?rs=$$" nsvId="https://www.ncbi.nlm.nih.gov/dbvar/variants/$$/" origName="https://www.ncbi.nlm.nih.gov/clinvar/variation/$$/" scoreLabel ClinVar Star-Rating (0-4) track clinvarMain - shortLabel ClinVar Short Variants - longLabel ClinVar Short Variants < 50bp - visibility pack parent clinvar + shortLabel ClinVar SNVs + longLabel ClinVar Short Variants < 50bp + visibility hide + group phenDis + itemRgb on priority 1 type bigBed 12 + + showCfg on + filterValues._clinSignCode BN|benign,LB|likely benign,CF|conflicting,PG|pathogenic,LP|likely pathogenic,UC|uncertain,OT|other + filterType._clinSignCode singleList + filterValues._originCode GERM|germline,SOM|somatic,GERMSOM|germline/somatic,NOVO|de novo,UNK|unknown + filterType._originCode singleList + filterLabel._originCode Alelle Origin + filterValues._allTypeCode SNV|single nucleotide variant - SNV,INS|insertion - INS,DEL|deletion - DEL,INDEL|insertion-deletion - INDEL,dupl|duplication - DUPL,OTH|other - OTH + filterType._allTypeCode singleList + filter._varLen 0 + filterByRange._varLen on + filterLimits._varLen 0:49 + filterValues.molConseq genic downstream transcript variant|genic downstream transcript variant,no sequence alteration|no sequence alteration,inframe indel|inframe indel,stop lost|stop lost,genic upstream transcript variant|genic upstream transcript variant,initiatior codon variant|initiatior codon variant,inframe insertion|inframe insertion,inframe deletion|inframe deletion,splice acceptor variant|splice acceptor variant,splice donor variant|splice donor variant,5 prime UTR variant|5 prime UTR variant,nonsense|nonsense,non-coding transcript variant|non-coding transcript variant,3 prime UTR variant|3 prime UTR variant,frameshift variant|frameshift variant,intron variant|intron variant,synonymous variant|synonymous variant,missense variant|missense variant,|unknown mouseOverField _mouseOver bigDataUrl /gbdb/$D/bbi/clinvar/clinvarMain.bb + urls rcvAcc="https://www.ncbi.nlm.nih.gov/clinvar/$$/" geneId="https://www.ncbi.nlm.nih.gov/gene/$$" snpId="https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=$$" nsvId="https://www.ncbi.nlm.nih.gov/dbvar/variants/$$/" origName="https://www.ncbi.nlm.nih.gov/clinvar/variation/$$/" + noScoreFilter on + searchIndex _dbVarSsvId track clinvarCnv - shortLabel ClinVar Long Variants - longLabel ClinVar Long Variants >= 50bp (mostly Copy-Number Variants) - visibility pack - type bigBed 12 + parent clinvar + shortLabel ClinVar CNVs + longLabel ClinVar Copy Number Variants > 50bp + visibility hide + type bigBed 12 + + itemRgb on + group phenDis priority 2 + filterValues._originCode GERM|germline,SOM|somatic,GERMSOM|germline/somatic,NOVO|de novo,UNK|unknown + filterType._originCode singleList + filterLabel._originCode Alelle Origin + filterValues._allTypeCode INS|insertion - INS,DEL|deletion - DEL,INDEL|insertion-deletion - INDEL,dupl|duplication - DUPL,OTH|other - OTH + filterType._allTypeCode singleList + filterValues._clinSignCode BN|benign,LB|likely benign,CF|conflicting,PG|pathogenic,LP|likely pathogenic,UC|uncertain,OT|other + filterType._clinSign singleList + 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/projects/SNP/snp_ref.cgi?rs=$$" nsvId="https://www.ncbi.nlm.nih.gov/dbvar/variants/$$/" origName="https://www.ncbi.nlm.nih.gov/clinvar/variation/$$/" + noScoreFilter on + searchIndex _dbVarSsvId + +searchTable clinvarCnv +searchType bigBed +searchDescription ClinVar Copy Number Variants + +searchTable clinvarMain +searchType bigBed +searchDescription ClinVar Copy Number Variants