--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/sort_chromosomal_position.sh	Thu Oct 22 09:18:30 2015 -0400
@@ -0,0 +1,26 @@
+#!/bin/bash
+
+#sort_chromosomal_position.sh $infile $chrcol $startcol $endcol $num_headerlines
+
+
+cp $1 inputfile.tsv
+chrcol=$2
+startcol=$3
+endcol=$4
+num_headerlines=$5
+outfile=$6
+
+#remember header 
+head -$num_headerlines inputfile.tsv > header.tsv
+
+#remove header
+sed -i "1,$num_headerlines d" inputfile.tsv
+
+#sort file
+sort -k ${chrcol},${chrcol}V -k${startcol},${startcol}n inputfile.tsv > tmpout.txt
+
+cat header.tsv tmpout.txt > $outfile
+
+
+
+