2ffc9d13a7475fbf6eb60a6b50d463ee11e7ff41
kate
  Wed Oct 25 18:06:54 2017 -0700
Implement V2 GTEx eQTL clusters as described in RM as 'permissive with ID'.  This adds Ensembl gene ID to schemas.  Also adding summary columns to cluster track (maxEffect, maxPvalue, effectType) to provide alternative to parsing comma-sep fields for table filtering. refs #15646

diff --git src/hg/lib/gtexEqtl.as src/hg/lib/gtexEqtl.as
index a053801..4838663 100644
--- src/hg/lib/gtexEqtl.as
+++ src/hg/lib/gtexEqtl.as
@@ -1,19 +1,20 @@
 table gtexEqtl
 "BED 9+ of expression Quantitative Trait Loci (eQTL). These are variants affecting gene expression"
     (
     string chrom;      "Reference sequence chromosome or scaffold"
     uint   chromStart; "Start position in chromosome"
     uint   chromEnd;   "End position in chromosome"
     string name;       "Variant/gene pair"
     uint   score;      "Score from 0-1000 (highest probabiliity in cluster * 1000)"
     char[1] strand;    "."
     uint thickStart;   "Start position"
     uint thickEnd;     "End position"
     uint reserved;     "R,G,B color: red +effect, blue -effect. Bright for high, pale for lower (cutoff effectSize 2.0 RPKM)."
     string variant;    "Variant (rsID or GTEx identifier if none)"
-    string gene;       "Target gene"
+    string geneId;     "Target gene identifier"
+    string gene;       "Target gene symbol"
     int distance;      "Distance from TSS"
     float effectSize;  "Effect size (FPKM)"
     float pValue;      "Nominal p-value"
-    float causalProb;  "Probability variant is in 95 percent credible set"
+    float causalProb;  "Probability variant is in high confidence causal set"
     )