1942abfbe86d5b3f5ed3ad0482a31a9354587e18
max
  Tue Mar 26 09:30:03 2024 -0700
preparing clinvar for somatic mutations, no ticket yet

diff --git src/hg/utils/otto/clinvar/clinvar.as src/hg/utils/otto/clinvar/clinvar.as
index d66aeb9..9ab1e80 100644
--- src/hg/utils/otto/clinvar/clinvar.as
+++ src/hg/utils/otto/clinvar/clinvar.as
@@ -1,45 +1,48 @@
 table clinVarBed
 "Browser extensible data (12 fields) plus information about a ClinVar entry. _clinSignCode has these possible values: BN=benign, LB=likely benign, CF=conflicting, PG=pathogenic, LP=likely pathogenic, UC=uncertain, OT=other"
     (
     string chrom;        "Chromosome (or contig, scaffold, etc.)"
     uint   chromStart;   "Start position in chromosome"
     uint   chromEnd;     "End position in chromosome"
     string name;         "Name of item"
     uint   score;      "Score from 0-1000"
     char[1] strand;    "+ or -"
     uint thickStart;   "Start of where display should be thick (start codon)"
     uint thickEnd;     "End of where display should be thick (stop codon)"
     uint reserved;     "Used as itemRgb as of 2004-11-22"
     int blockCount;    "Number of blocks"
     int[blockCount] blockSizes; "Comma separated list of block sizes"
     int[blockCount] chromStarts; "Start positions relative to chromStart"
     lstring origName;         "Link to ClinVar with Variant ID"
     string clinSign;         "Clinical significance"
     string reviewStatus;   "Review Status"
     string type;         "Type of Variant"
     string geneId;         "Gene Symbol"
     string molConseq;         "Molecular Consequence"
     string snpId;         "dbSNP ID"
     string nsvId;         "dbVar ID"
     lstring rcvAcc;         "ClinVar Allele Submission"
     string testedInGtr;         "Genetic Testing Registry"
     lstring phenotypeList;         "Phenotypes"
     lstring phenotype;         "Phenotype identifiers"
     string origin;         "Allele origin"
     string assembly;         "Genome assembly"
     string cytogenetic;         "Cytogenetic status"
     lstring _jsonHgvsTable;         "HGVS names"
     lstring _hgvsProt;         "Protein HGVS"
     string numSubmit;         "Number of submitters"
     string lastEval;         "Last evaluation"
     string guidelines;         "Guidelines"
     lstring otherIds;         "Other identifiers (ClinGen, OMIM, etc.)"
     lstring _mouseOver;        "Mouse over text"
+    string vcfDesc;            "VCF position|Can differ from ClinVar position due to left/right shifting rules"
+    string somImpactDesc;       "Somatic Impact"
+    string oncogenDesc;       "Oncogen"
     string _clinSignCode;        "Clinical Significance"
     string _originCode;        "Allele Origin Code"
     string _allTypeCode;        "Variation Type"
     uint _varLen;            "Variant Length in base pairs"
     uint _starCount;         "Number of stars"
     int _variantId;           "ClinVar variant ID"
     string _dbVarSsvId;           "dbVar SSV ID"
     )