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.ra src/hg/makeDb/trackDb/human/trackDb.clinvar.ra
index 0309cc7..91d1d48 100644
--- src/hg/makeDb/trackDb/human/trackDb.clinvar.ra
+++ src/hg/makeDb/trackDb/human/trackDb.clinvar.ra
@@ -8,63 +8,63 @@
 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
-        filterType._clinSignCode singleList
-        filterValues._originCode GERM|germline,SOM|somatic,GERMSOM|germline/somatic,NOVO|de novo,UNK|unknown
-        filterType._originCode singleList
+        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 singleList
+        filterType._allTypeCode multiple
         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
         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
+        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 singleList
+        filterType._allTypeCode multiple
         filterValues._clinSignCode BN|benign,LB|likely benign,CF|conflicting,PG|pathogenic,LP|likely pathogenic,UC|uncertain,OT|other
-        filterType._clinSign singleList
+        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