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comparison vcf2gvf.sh @ 0:21053f7f9ed1 draft

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First upload of PCR Marker tools
author john-mccallum
date Thu, 14 Jun 2012 19:29:26 -0400
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-1:000000000000 0:21053f7f9ed1
1 #!/bin/sh
2 ##convert vcf to gvf
3 ##NOTE This is a very simple basic parser for a complex format.
4
5 ##usage vcf2gvf.sh <vcf file> <outputfile>
6
7 #Copyright 2012 John McCallum & Leshi Chen
8 #New Zealand Institute for Plant and Food Research
9
10 #New Zealand Institute for Plant and Food Research
11 #This program is free software: you can redistribute it and/or modify
12 # it under the terms of the GNU General Public License as published by
13 # the Free Software Foundation, either version 3 of the License, or
14 # (at your option) any later version.
15 #
16 # This program is distributed in the hope that it will be useful,
17 # but WITHOUT ANY WARRANTY; without even the implied warranty of
18 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
19 # GNU General Public License for more details.
20 #
21 # You should have received a copy of the GNU General Public License
22 # along with this program. If not, see <http://www.gnu.org/licenses/>.
23
24
25
26 inputfile=$1
27 outputfile=$2
28
29 echo "##gvf-version 1.05" > $outputfile
30
31 awk '
32 BEGIN {OFS="\t"}
33
34 ##get feature type
35 {if (index($8,"INDEL")== 1) {type="INDEL"} else {type="SNP"} }
36 ##get feature length
37 {if (type=="SNP")
38 {feat_length=1}
39 else {feat_length=length($4)}
40 }
41 {end=($2+feat_length)}
42
43 !/^#/ { print $1 ,"SAMTOOLS",type,$2,end,$6,".",".","ID="$1":SAMTOOLS:"type":"$2";Variant_seq="$5";Reference_seq="$4";"$8}
44
45 END {print ""}
46 ' "$inputfile" > "$outputfile"