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author saskia-hiltemann
date Mon, 03 Aug 2015 05:01:15 -0400
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<tool id="vcf2lv" name="VCF-2-VariantList" version="1">
 	<description> convert VCF file to CG-compatible variant list </description>
  
  	<command interpreter="bash"> 
  		vcf2lv.sh $vcffile $outputfile	
  	</command>

  	<inputs>
  		<param name="vcffile" type="data" label="Select vcf file" />
  		<param name="fname" type="text" value="" label="Prefix for your output file" help="Optional"/>	
  	</inputs>

	<outputs>
  		<data format="tabular" name="outputfile" label="${fname} VCF-2-VariantList conversion"/>
  	</outputs>
  	
  	<help>  
**what it does**

Converts a VCF file containing small variants (SNVs, indels and substitutions) to a Complete Genomics type variantlist.
		
After conversion, the file can be used as input to the Virtual Normal filtering pipeline. 



	</help>
</tool>