90722fe965a89529d622dc70225dea8cf3924e32
chmalee
  Tue Aug 4 16:53:00 2020 -0700
Stage genome in a bottle trio vcf track, refs #25873

diff --git src/hg/makeDb/giab/mergeVcfs.sh src/hg/makeDb/giab/mergeVcfs.sh
new file mode 100755
index 0000000..a707d20
--- /dev/null
+++ src/hg/makeDb/giab/mergeVcfs.sh
@@ -0,0 +1,20 @@
+#!/bin/bash
+set -beEu -o pipefail
+for db in hg38 hg19
+do
+    for pop in AshkenazimTrio ChineseTrio
+    do
+        mkdir -p /gbdb/${db}/giab/${pop}/
+        pushd ${db}/${pop}/
+        if [ ${pop} == "ChineseTrio" ]
+        then
+            bcftools merge -o merged.vcf HG005*.vcf.gz HG006.vcf.gz HG007.vcf.gz
+        else
+            bcftools merge -o merged.vcf HG*.vcf.gz
+        fi
+        bgzip -c merged.vcf > merged.vcf.gz
+        tabix -p vcf merged.vcf.gz
+        ln -s `pwd`/merged.vcf.* /gbdb/${db}/giab/${pop}
+        popd
+    done
+done