4e6eb7db020f87bdc9f63f347cee9a080251f0fa
braney
  Wed May 1 15:00:06 2019 -0700
clean up GDC Cancer AS file

diff --git src/hg/lib/gdcCancer.as src/hg/lib/gdcCancer.as
new file mode 100644
index 0000000..7e96585
--- /dev/null
+++ src/hg/lib/gdcCancer.as
@@ -0,0 +1,41 @@
+table gdcCancer
+"somatic variants converted from MAF files obtained through the NCI GDC"
+    (
+    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"
+    string sampleCount;    "Number of samples with this variant"
+    string freq;                    "Variant frequency"
+    lstring Hugo_Symbol;            "Hugo symbol"
+    lstring Entrez_Gene_Id;         "Entrez Gene Id"
+    lstring Variant_Classification; "Class of variant"
+    lstring Variant_Type;           "Type of variant"
+    lstring Reference_Allele;       "Reference allele"
+    lstring Tumor_Seq_Allele1;      "Tumor allele 1"
+    lstring Tumor_Seq_Allele2;      "Tumor allele 2"
+    lstring dbSNP_RS;               "dbSNP RS number"
+    lstring dbSNP_Val_Status;       "dbSNP validation status"
+    lstring days_to_death;          "Number of days till death"
+    lstring cigarettes_per_day;     "Number of cigarettes per day"
+    lstring weight;                 "Weight"
+    lstring alcohol_history;        "Any alcohol consumption?"
+    lstring alcohol_intensity;      "Frequency of alcohol consumption"
+    lstring bmi;                    "Body mass index"
+    lstring years_smoked;           "Number of years smoked"
+    lstring height;                 "Height"
+    lstring gender;                 "Gender"
+    lstring project_id;             "TCGA Project id"
+    lstring ethnicity;              "Ethnicity"
+    lstring Tumor_Sample_Barcode;   "Tumor sample barcode"
+    lstring Matched_Norm_Sample_Barcode;  "Matcheds normal sample barcode"
+    lstring case_id;                "Case ID number"
+)