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/gtexEqtlCluster.as src/hg/lib/gtexEqtlCluster.as
index 779cd66..dd2592f 100644
--- src/hg/lib/gtexEqtlCluster.as
+++ src/hg/lib/gtexEqtlCluster.as
@@ -1,16 +1,20 @@
 table gtexEqtlCluster
 "BED5+ of eQTLs (variants affecting gene expression) with a target (gene or tissue), and lists of values related to combined factors (e.g. tissues or genes)
     (
     string chrom;      "Reference sequence chromosome or scaffold"
     uint   chromStart; "Start position in chromosome"
     uint   chromEnd;   "End position in chromosome"
     string name;       "Name of variant (rsID or GTEx identifier if none)"
     uint   score;      "Score from 0-1000"
+    string targetId;   "Identifier of target (gene or tissue)
     string target;     "Name of target (gene or tissue)
     int distance;      "Distance from TSS"
+    float maxEffect;   "Maximum absolute value effect size in cluster"
+    char[1] effectType; "+, -, 0 (for mixed)"
+    float maxPvalue;   "Maximum -log10 pValue in cluster"
     uint expCount;     "Number of experiment values"
     string[expCount] expNames; "Comma separated list of experiment names (e.g. tissue or gene)"
     float[expCount] expScores; "Comma separated list of effect size values"
     float[expCount] expPvals; "Comma separated list of -log10 transformed p-values"
-    float[expCount] expProbs; "Comma separated list of probabilities variant is causal"
+    float[expCount] expProbs; "Comma separated list of probabilities variant is in high confidence causal set"
     )