633cc56e1b1043b0ab6e1fd0e9b90154e2c03c0c
hiram
  Mon Apr 20 13:00:51 2026 -0700
document procedure for import of VGP 577-way maf result refs #34370

diff --git src/hg/makeDb/doc/vgp577way/mkNbeds.sh src/hg/makeDb/doc/vgp577way/mkNbeds.sh
new file mode 100755
index 00000000000..bd70656fb83
--- /dev/null
+++ src/hg/makeDb/doc/vgp577way/mkNbeds.sh
@@ -0,0 +1,59 @@
+#!/bin/bash
+
+mkdir -p nBedDir
+
+grep "^GC" ../species.list | while read acc
+do
+  gcX="${acc:0:3}"
+  d0="${acc:4:3}"
+  d1="${acc:7:3}"
+  d2="${acc:10:3}"
+  srcDir="/hive/data/genomes/asmHubs/${gcX}/${d0}/${d1}/${d2}/${acc}"
+  if [ -d "${srcDir}" ]; then
+    twoBit="${srcDir}/${acc}.2bit"
+    if [ -s "${twoBit}" ]; then
+      twoBitInfo -nBed ${twoBit} nBedDir/${acc}.bed
+      ln -s nBedDir/${acc}.bed ./
+    else
+      printf "ERROR: can not find twoBit:\n%s\n" "${twoBit}"
+      exit 255
+    fi
+  else
+    printf "ERROR: can not find source directory:\n%s\n" "${srcDir}"
+    exit 255
+  fi
+done
+
+# GCF_963930625.1
+# GCF_964237555.1
+# hg38
+# hs1
+# mm39
+
+grep -v "^GC" ../species.list | while read db
+do
+  srcDir="/hive/data/genomes/${db}"
+  if [ -d "${srcDir}" ]; then
+    twoBit="${srcDir}/${db}.2bit"
+    if [ -s "${twoBit}" ]; then
+      twoBitInfo -nBed ${twoBit} nBedDir/${db}.bed
+      ln -s nBedDir/${db}.bed ./
+    else
+      printf "ERROR: can not find 2bit:\n%s\n" "${twoBit}"
+      exit 255
+    fi
+  else
+    printf "ERROR: can not find source directory:\n%s\n" "${srcDir}"
+    exit 255
+  fi
+done
+
+ls *.bed > nBeds
+
+wc -l nBeds sizes
+
+# GCF_963930625.1
+# GCF_964237555.1
+# hg38
+# hs1
+# mm39