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