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1 <tool id="vcf2lv" name="VCF-2-VariantList" version="1">
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2 <description> convert VCF file to CG-compatible variant list </description>
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3
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4 <command interpreter="bash">
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5 vcf2lv.sh $vcffile $outputfile
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6 </command>
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7
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8 <inputs>
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9 <param name="vcffile" type="data" label="Select vcf file" />
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10 <param name="fname" type="text" value="" label="Prefix for your output file" help="Optional"/>
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11 </inputs>
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12
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13 <outputs>
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14 <data format="tabular" name="outputfile" label="${fname} VCF-2-VariantList conversion"/>
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15 </outputs>
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16
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17 <help>
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18 **what it does**
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19
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20 Converts a VCF file containing small variants (SNVs, indels and substitutions) to a Complete Genomics type variantlist.
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21
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22 After conversion, the file can be used as input to the Virtual Normal filtering pipeline.
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23
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24
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25
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26 </help>
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27 </tool>
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