initial commit

rkawaguc · Dec 2, 2016 · 272e2b7 · 272e2b7
1 parent f039545
commit 272e2b7
Showing 1 changed file with 11 additions and 0 deletions.
diff --git a/bin/getbedgraph.sh b/bin/getbedgraph.sh
@@ -0,0 +1,11 @@
+#!/bin/bash
+#$ -S /bin/bash
+#$ -l h_data=4G
+#$ -cwd
+
+input=$1
+ref=$2
+out=$3 
+genomeCoverageBed -bg -ibam $input -g $ref -split -bg  > ${input}.temp
+sed 's/^/chr/' ${input}.temp >$out.bedgraph
+rm ${input}.temp