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comparison vcf2gvf.xml @ 5:b321e0517be3 draft

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author ben-warren
date Thu, 22 May 2014 20:30:19 -0400
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4:be070a68521e 5:b321e0517be3
1 <?xml version="1.0"?>
2 <tool id="vcf2gvf_1" name="VCF to GFF3">
3 <description>convert vcf to gvf/gff3</description>
4 <command interpreter="bash">vcf2gvf.sh $inputFile $outputfile</command>
5 <inputs>
6 <param format="vcf" name="inputFile" type="data" label="Input vcf File" help="vcf file from mpileup" />
7 </inputs>
8 <outputs>
9 <data format="gff3" name="outputfile" />
10
11 </outputs>
12 <help>
13 This tool provides a simple conversion from vcf to gvf.
14
15 It is intended for use with Freebayes or with Samtools mpileup
16
17 Be sure to read the documentation to determine if it meets your requirements.
18
19 * vcf documentation at http://samtools.sourceforge.net/samtools.shtml#6
20 * GVF/GFF3 at http://www.sequenceontology.org/resources/gvf.html
21 * Freebayes https://github.com/ekg/freebayes
22
23
24
25 **input**
26
27 ::
28
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
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
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
32
33
34 **output**
35
36
37 ::
38
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
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
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
42
43
44
45 -----------------------
46
47 *If you use this tool please cite:*
48
49 A Toolkit For Bulk PCR-Based Marker Design From Next-Generation Sequence Data:
50 Application For Development Of A Framework Linkage Map In Bulb Onion (*Allium cepa* L.)
51 (2012)
52
53 Samantha Baldwin, Roopashree Revanna, Susan Thomson, Meeghan Pither-Joyce, Kathryn Wright,
54 Ross Crowhurst, Mark Fiers, Leshi Chen, Richard MacKnight, John A. McCallum
55
56
57 </help>
58 </tool>