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1 <?xml version="1.0"?>
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2 <tool id="vcf2gvf_1" name="VCF to GFF3">
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3 <description>convert vcf to gvf/gff3</description>
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4 <command interpreter="bash">vcf2gvf.sh $inputFile $outputfile</command>
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5 <inputs>
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6 <param format="vcf" name="inputFile" type="data" label="Input vcf File" help="vcf file from mpileup" />
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7 </inputs>
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8 <outputs>
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9 <data format="gff3" name="outputfile" />
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10
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11 </outputs>
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12 <help>
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13 This tool provides a simple conversion from vcf to gvf.
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14
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15 It is intended for use with Freebayes or with Samtools mpileup
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16
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17 Be sure to read the documentation to determine if it meets your requirements.
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18
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19 * vcf documentation at http://samtools.sourceforge.net/samtools.shtml#6
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20 * GVF/GFF3 at http://www.sequenceontology.org/resources/gvf.html
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21 * Freebayes https://github.com/ekg/freebayes
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22
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23
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24
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25 **input**
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26
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27 ::
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28
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29 PGSC0003DMB000000010 2042429 . C A 44.6 . DP=10;VDB=0.0118;AF1=0.8295;AC1=7;DP4=2,1,3,4;MQ=20;FQ=8.78;PV4=1,5.2e-10,1,1 GT:PL:DP:GQ 0/1:14,0,42:5:23 1/1:27,6,0:2:9 1/1:15,3,0:1:7 1/1:30,6,0:2:9
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30 PGSC0003DMB000000038 1756646 . G A 3.69 . DP=15;VDB=0.0166;AF1=0.495;AC1=4;DP4=3,7,2,2;MQ=20;FQ=5.6;PV4=0.58,3.8e-09,1,0.31 GT:PL:DP:GQ 0/1:20,3,0:1:6 0/1:9,0,67:7:8 0/0:0,15,82:5:17 0/1:16,3,0:1:5
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31 PGSC0003DMB000000064 1916664 . T C 8.12 . DP=4;VDB=0.0151;AF1=1;AC1=8;DP4=0,0,0,3;MQ=20;FQ=-29.5 GT:PL:DP:GQ 1/1:14,3,0:1:5 1/1:0,0,0:0:3 1/1:13,3,0:1:5 1/1:15,3,0:1:5
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32
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33
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34 **output**
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35
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36
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37 ::
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38
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39 PGSC0003DMB000000010 samtools SNP 2042429 2042430 44.6 . . ID=PGSC0003DMB000000010:SAMTOOLS:SNP:2042429;Variant_seq=A;Reference_seq=C;DP=10;VDB=0.0118;AF1=0.8295;AC1=7;DP4=2,1,3,4;MQ=20;FQ=8.78;PV4=1,5.2e-10,1,1
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40 PGSC0003DMB000000038 samtools SNP 1756646 1756647 3.69 . . ID=PGSC0003DMB000000038:SAMTOOLS:SNP:1756646;Variant_seq=A;Reference_seq=G;DP=15;VDB=0.0166;AF1=0.495;AC1=4;DP4=3,7,2,2;MQ=20;FQ=5.6;PV4=0.58,3.8e-09,1,0.31
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41 PGSC0003DMB000000064 samtools SNP 1916664 1916665 8.12 . . ID=PGSC0003DMB000000064:SAMTOOLS:SNP:1916664;Variant_seq=C;Reference_seq=T;DP=4;VDB=0.0151;AF1=1;AC1=8;DP4=0,0,0,3;MQ=20;FQ=-29.5
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42
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43
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44
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45 -----------------------
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46
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47 *If you use this tool please cite:*
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48
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49 A Toolkit For Bulk PCR-Based Marker Design From Next-Generation Sequence Data:
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50 Application For Development Of A Framework Linkage Map In Bulb Onion (*Allium cepa* L.)
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51 (2012)
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52
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53 Samantha Baldwin, Roopashree Revanna, Susan Thomson, Meeghan Pither-Joyce, Kathryn Wright,
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54 Ross Crowhurst, Mark Fiers, Leshi Chen, Richard MacKnight, John A. McCallum
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55
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56
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57 </help>
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58 </tool>
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