<?xml version="1.0"?>
<tool id="vcf2gvf_1" name="VCF to GFF3">
  <description>convert vcf to gvf/gff3</description>
  <command interpreter="bash">vcf2gvf.sh  $inputFile  $outputfile</command>
  <inputs>
    <param format="vcf" name="inputFile" type="data" label="Input vcf File" help="vcf file from mpileup" />
  </inputs>
  <outputs>
<data format="gff3" name="outputfile" /> 

  </outputs>
<help>
This tool provides a simple conversion from vcf to gvf.

It is intended for use with Freebayes or with Samtools mpileup 

Be sure to read the documentation to determine if it meets your requirements.

* vcf documentation at http://samtools.sourceforge.net/samtools.shtml#6
* GVF/GFF3 at http://www.sequenceontology.org/resources/gvf.html
* Freebayes https://github.com/ekg/freebayes



**input**

::

	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
	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
	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


**output**


::

	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
	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
	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



-----------------------

*If you use this tool please cite:*

A Toolkit For Bulk PCR-Based Marker Design From Next-Generation Sequence Data: 
Application For  Development Of A Framework Linkage Map In Bulb Onion (*Allium cepa* L.)
(2012)

Samantha Baldwin, Roopashree Revanna, Susan Thomson, Meeghan Pither-Joyce, Kathryn Wright, 
Ross Crowhurst, Mark Fiers, Leshi Chen, Richard MacKnight, John A. McCallum


</help>
</tool>