--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/2.4/script/Subset_targets.sh	Mon Jun 02 07:35:53 2014 -0400
@@ -0,0 +1,23 @@
+#!/bin/sh
+#$ -V
+#$ -cwd
+#$ -q 1-day
+#$ -m ae
+#$ -M hart.steven@mayo.edu
+#$ -l h_vmem=1G
+#$ -l h_stack=10M
+BAM=$1
+TARGET_BED=$2
+SAMPLE_NUMBER=$3
+
+#cat $HEADER > out.${SAMPLE_NUMBER}.sam
+samtools view -L $TARGET_BED $BAM|
+ perl -ane '
+ next if ($F[10]=~/#/);
+ $minSize=1000;
+ if( $F[1] & 8 || $F[1] & 4 ||  $F[8] == 0 || abs($F[8]) > $minSize || $F[5] =~/S/){
+ $rName=join("","@",@F[0]);
+  print join ("\n",$rName,$F[9],"+",@F[10])."\n";
+};
+ ' >> out.${SAMPLE_NUMBER}.fq
+echo "Done with $BAM `date`"