--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/vcf2gvf.sh	Thu May 22 20:30:19 2014 -0400
@@ -0,0 +1,47 @@
+#!/bin/sh
+##convert vcf to gvf
+##NOTE This is a very simple basic parser for a complex format.
+#It is intended for use with mpileup output where -g or -u flags are NOT used.
+
+##usage vcf2gvf.sh <vcf file> <outputfile>
+
+#Copyright 2012 John McCallum & Leshi Chen
+#New Zealand Institute for Plant and Food Research
+
+#New Zealand Institute for Plant and Food Research
+#This program is free software: you can redistribute it and/or modify
+#     it under the terms of the GNU General Public License as published by
+#    the Free Software Foundation, either version 3 of the License, or
+#    (at your option) any later version.
+#
+#    This program is distributed in the hope that it will be useful,
+#    but WITHOUT ANY WARRANTY; without even the implied warranty of
+#    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+#    GNU General Public License for more details.
+#
+#    You should have received a copy of the GNU General Public License
+#    along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
+
+
+inputfile=$1
+outputfile=$2
+
+echo  "##gvf-version 1.05" > $outputfile
+
+awk '
+BEGIN {OFS="\t"}
+
+##get feature type 
+{if (index($8,"INDEL")== 1) {type="INDEL"} else {type="SNP"} }
+##get feature length
+{if (type=="SNP") 
+    {feat_length=1}
+    else {feat_length=length($4)} 
+}
+{end=($2+feat_length)}
+
+!/^#/  { print $1 ,"SAMTOOLS",type,$2,end,$6,".",".","ID="$1":SAMTOOLS:"type":"$2";Variant_seq="$5";Reference_seq="$4";"$8}
+
+END {print ""} 
+' "$inputfile" > "$outputfile"
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