Mercurial > repos > john-mccallum > pcr_markers
comparison vcf2gvf.xml @ 0:21053f7f9ed1 draft
First upload of PCR Marker tools
author | john-mccallum |
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date | Thu, 14 Jun 2012 19:29:26 -0400 |
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-1:000000000000 | 0:21053f7f9ed1 |
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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 Be sure to read the documentation to determine if it meets your requirements. | |
16 | |
17 * vcf documentation at http://samtools.sourceforge.net/samtools.shtml#6 | |
18 * GVF/GFF3 at http://www.sequenceontology.org/resources/gvf.html | |
19 | |
20 | |
21 | |
22 **input** | |
23 | |
24 :: | |
25 | |
26 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 | |
27 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 | |
28 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 | |
29 | |
30 | |
31 **output** | |
32 | |
33 | |
34 :: | |
35 | |
36 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 | |
37 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 | |
38 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 | |
39 | |
40 | |
41 | |
42 ----------------------- | |
43 | |
44 *If you use this tool please cite:* | |
45 | |
46 A Toolkit For Bulk PCR-Based Marker Design From Next-Generation Sequence Data: | |
47 Application For Development Of A Framework Linkage Map In Bulb Onion (*Allium cepa* L.) | |
48 (2012) | |
49 | |
50 Samantha Baldwin, Roopashree Revanna, Susan Thomson, Meeghan Pither-Joyce, Kathryn Wright, | |
51 Ross Crowhurst, Mark Fiers, Leshi Chen, Richard MacKnight, John A. McCallum | |
52 | |
53 | |
54 </help> | |
55 </tool> |