95ac7607e394e7daab5bec99238e7db860b4849b
lrnassar
  Fri Aug 13 17:09:31 2021 -0700
Updating clinvar filters and clarifying the clinvar interp desc page to explain bead sizes, refs #27991

diff --git src/hg/makeDb/trackDb/human/trackDb.clinvar.alpha.ra src/hg/makeDb/trackDb/human/trackDb.clinvar.alpha.ra
deleted file mode 100644
index dc7bbfc..0000000
--- src/hg/makeDb/trackDb/human/trackDb.clinvar.alpha.ra
+++ /dev/null
@@ -1,96 +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/projects/SNP/snp_ref.cgi?rs=$$" nsvId="https://www.ncbi.nlm.nih.gov/dbvar/variants/$$/" origName="https://www.ncbi.nlm.nih.gov/clinvar/variation/$$/"
-scoreLabel ClinVar Star-Rating (0-4)
-
-        track clinvarMain
-        parent clinvar
-        shortLabel ClinVar SNVs
-        longLabel ClinVar Short Variants < 50bp
-        visibility hide
-        group phenDis
-        itemRgb on
-        priority 1
-        type bigBed 12 +
-        showCfg on
-        filterValues._clinSignCode BN|benign,LB|likely benign,CF|conflicting,PG|pathogenic,LP|likely pathogenic,UC|uncertain,OT|other,VUS|vus
-        filterType._clinSignCode multiple
-        filterValues._originCode GERM|germline,SOM|somatic,GERMSOM|germline/somatic,UNK|unknown
-        filterType._originCode multiple
-        filterLabel._originCode Alelle Origin
-        filterValues._allTypeCode SNV|single nucleotide variant - SNV,INS|insertion - INS,DEL|deletion - DEL,INDEL|insertion-deletion - INDEL,dupl|duplication - DUPL,OTH|other - OTH
-        filterType._allTypeCode multiple
-        filter._varLen 0
-        filterByRange._varLen on
-        filterLimits._varLen 0:49
-        filterType.molConseq multiple
-        filterValues.molConseq genic downstream transcript variant|genic downstream transcript variant,no sequence alteration|no sequence alteration,inframe indel|inframe indel,stop lost|stop lost,genic upstream transcript variant|genic upstream transcript variant,initiatior codon variant|initiatior codon variant,inframe insertion|inframe insertion,inframe deletion|inframe deletion,splice acceptor variant|splice acceptor variant,splice donor variant|splice donor variant,5 prime UTR variant|5 prime UTR variant,nonsense|nonsense,non-coding transcript variant|non-coding transcript variant,3 prime UTR variant|3 prime UTR variant,frameshift variant|frameshift variant,intron variant|intron variant,synonymous variant|synonymous variant,missense variant|missense variant,|unknown
-        mouseOverField _mouseOver
-        bigDataUrl /gbdb/$D/bbi/clinvar/clinvarMain.bb
-        urls rcvAcc="https://www.ncbi.nlm.nih.gov/clinvar/$$/" 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
-        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 multiple
-        filterLabel._originCode Alelle Origin
-        filterValues._allTypeCode INS|insertion - INS,DEL|deletion - DEL,INDEL|insertion-deletion - INDEL,dupl|duplication - DUPL,OTH|other - OTH
-        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/projects/SNP/snp_ref.cgi?rs=$$" nsvId="https://www.ncbi.nlm.nih.gov/dbvar/variants/$$/" origName="https://www.ncbi.nlm.nih.gov/clinvar/variation/$$/"
-        noScoreFilter on
-        searchIndex _dbVarSsvId
-
-        track clinvarSubLolly
-        parent clinvar
-        shortLabel ClinVar interp
-        longLabel ClinVar SNVs submitted interpretations and evidence
-        bigDataUrl /gbdb/$D/clinvarSubLolly/clinvarSubLolly.bb
-        xrefDataUrl /gbdb/$D/clinvarSubLolly/clinvarSub.bb
-        type bigLolly
-        group phenDis
-        lollySizeField 10
-        yAxisNumLabels off
-        lollyNoStems on
-        configurable off
-        yAxisLabel.0 0 on 150,150,150 OTH
-        yAxisLabel.1 1 on 150,150,150 B
-        yAxisLabel.2 2 on 150,150,150 LB
-        yAxisLabel.3 3 on 150,150,150 VUS
-        yAxisLabel.4 4 on 150,150,150 LP
-        yAxisLabel.5 5 on 150,150,150 P
-        lollyMaxSize 10
-        viewLimits 0:5
-        mouseOverField _mouseOver
-        urls rcvAcc="https://www.ncbi.nlm.nih.gov/clinvar/$$/" geneId="https://www.ncbi.nlm.nih.gov/gene/$$" snpId="https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=$$" 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 
-
-searchTable clinvarMain
-searchType bigBed
-searchDescription ClinVar Copy Number Variants