71b469a98a76ff8be8ab09ff421471f0e4d71351
chmalee
  Tue Mar 3 14:48:45 2020 -0800
Quick run up of gnomAD structural variants track for hg19, refs #24179

diff --git src/hg/makeDb/gnomad/gnomadSvToUcsc.awk src/hg/makeDb/gnomad/gnomadSvToUcsc.awk
new file mode 100755
index 0000000..518c451
--- /dev/null
+++ src/hg/makeDb/gnomad/gnomadSvToUcsc.awk
@@ -0,0 +1,51 @@
+#!/usr/bin/awk -f
+# turn a gnomad SV file to ucsc bigBed 9+
+
+BEGIN {
+    FS="\t";
+    OFS="\t";
+}
+
+{
+chrom=$1
+start=$2
+end=$3
+origName=$4
+svtype=$5
+
+split($4,a,"_")
+name=a[3] "_" a[4] "_" a[5]
+color=""
+
+switch(svtype) {
+    case "BND":
+        color = "154,182,160"
+        break
+    case "CPX":
+        color = "182,239,195"
+        break
+    case "CTX":
+        color = "154,182,160"
+        break
+    case "DEL":
+        color = "231,154,144"
+        break
+    case "DUP":
+        color = "143,184,214"
+        break
+    case "INS":
+        color = "231,183,237"
+        break
+    case "INV":
+        color = "250,199,140"
+        break
+    case "MCNV":
+        color = "183,170,214"
+        break
+    default:
+        color = "154,182,160"
+        break
+}
+
+print chrom, start, end, name, 0, ".", start, end, color, svtype
+}