032ef09c0d89b90b4967379956b2f8d9446575b9
ceisenhart
  Thu May 11 11:05:18 2017 -0700
Cosmic tracks scripts, code changes and documentation, refs #14461 and #18919

diff --git src/hg/lib/cosmicNew.as src/hg/lib/cosmicNew.as
index 83be3c0..5af51ff 100644
--- src/hg/lib/cosmicNew.as
+++ src/hg/lib/cosmicNew.as
@@ -1,18 +1,39 @@
 table cosmicNew
-"Catalog of Somatic Mutations in Cancer (COSMIC)"
+"Bed representation of the Catalog of Somatic Mutations in Cancer (COSMIC)"
     (
     string chrom;          "Reference sequence chromosome or scaffold"
     uint   chromStart;     "Start position in chromosome"
     uint   chromEnd;       "End position in chromosome"
     string name;           "COSMIC mutation ID"
+    char[1] strand;        "+ or - for strand. Use . if not applicable"
     string geneName;       "Gene: HUGO symbol, mir-* ID, etc" 
     string transcriptAcc;  "ENST, NM_, XM_ or other transcript accession"
-    string mutDescription; "description of effect of variant on gene"
-    string hgvsCds;        "HGVS variant nomenclature representation of mutation in CDS"
-    string hgvsProt;       "HGVS variant nomenclature representation of mutation in protein"
-    lstring ntChange;      "nucleotide sequence change"
-    lstring aaChange;      "amino acid sequence change"
-    string tumorSite;      "organ or tissue from which tumor sample was taken"
-    int mutatedSamples;    "number of samples with the mutation"
-    int examinedSamples;   "number of samples examined"
+    int geneCdsLength;     "Length of the gene (base pair) counts"
+    int geneId;            "If gene is in HGNC, this id helps linking it to HGNC"
+    string sampleName;     "A sample is an instance of a portion of a tumour being examined for mutations"
+    int sampleId;          "A sample id is used to identify a sample within the COSMIC database"
+    int idTumor;           "A number of samples can be taken from a single tumour and a number of tumours can be obtained from one individual"
+    string primSite;       "Primary site of organ or tissue from which tumor sample was taken"
+    string siteSubtype1;   "Subtype 1 site of organ or tissue from which tumor sample was taken"
+    string siteSubtype2;   "Subtype 2 site of organ or tissue from which tumor sample was taken"
+    string siteSubtype3;   "Subtype 3 site of organ or tissue from which tumor sample was taken"
+    string primHistology;  "Primary histology of organ or tissue from which tumor sample was taken"
+    string histSubtype1;   "Subtype 1 histology of organ or tissue from which tumor sample was taken"
+    string histSubtype2;   "Subtype 2 histology of organ or tissue from which tumor sample was taken"
+    string histSubtype3;   "Subtype 3 histology of organ or tissue from which tumor sample was taken"
+    lstring ntChange;      "Nucleotide sequence change"
+    lstring aaChange;      "Amino acid sequence change"
+    string mutDescription; "Description of effect of variant on gene"
+    string mutZygosity;    "Information on whether the mutation was reported to be homozygous , heterozygous or unknown within the sample"
+    string loh;            "LOH Information on whether the gene was reported to have loss of heterozygosity in the sample, yes, no or unknown."
+    char[1] snp;           "All the known SNPs are flagged as 'y' defined by the 1000 genomes project, dbSNP and a panel of 378 normal (non-cancer) samples from Sanger CGP sequencing"
+    string resMut;         "Resistant mutation, mutation confers drug resistance"
+    string fathmmPred;     "FATHMM (Functional Analysis through Hidden Markov Models) prediction"
+    float fathmmScore;     "FATHMM score, a pvalue ranging from 0 to 1. Greater than .5 is signicant, less is benign"
+    string mutSomStat;     "Mutation somatic status"
+    int pubmedId;          "The PUBMED id for the paper the sample was noted in"
+    string studyIds;       "Lists the unique Ids of studies that have involved this sample."
+    string samSource;      "Describes where the sample has originated from"
+    string tumSource;      "Describes the tumor type"
+    float age;             "Age of the sample (if provided)"
     )