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1 <tool id="varscan" name="VarScan Readcount" version="2.4.4">
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2 <description>To use varscan readcount tool</description>
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3
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4 <requirements>
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5 <requirement type="package" version="2.4.4">varscan</requirement>
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6 </requirements>
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7
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8 <stdio>
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9 <regex match="Exception" source="both" level="fatal" description="Tool exception"/>
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10 <regex match=".*" source="both" level="log" description="tool progress"/>
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11 </stdio>
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12
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13 <version_command><![CDATA[
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14 varscan 2>&1 | head -n 1
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15 ]]></version_command>
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16
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17 <command><![CDATA[
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18 varscan readcounts ${input} --min-coverage ${min_cov} --min-base-qual ${min_base_qual} --output-file ${output}
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19 ]]></command>
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20
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21 <inputs>
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22 <param format="pileup" name="input" type="data" label="Pileup dataset" help=""/>
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23 <param name="min_cov" type="integer" value="1" min="1" max="2000" label="Minimum read depth" help="Minimum depth at a position to make a call [1]"/>
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24 <param name="min_base_qual" type="integer" value="20" min="1" max="500" label="Minimum base quality" label="Minimum base quality at a position to count a read [20]"/>
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25 </inputs>
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26
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27 <outputs>
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28 <data name="output" format="vcf"/>
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29 </outputs>
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30
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31 <help>
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32
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33 command: varscan readcounts --help
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34
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35 Min coverage: 1
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36 Min base qual: 20
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37 USAGE: java -jar VarScan.jar readcounts [pileup] OPTIONS
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38 OPTIONS:
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39 --variants-file A list of variants at which to report readcounts
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40 --output-file Output file to contain the readcounts
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41 --min-coverage Minimum read depth at a position to make a call [1]
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42 --min-base-qual Minimum base quality at a position to count a read [20]
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43
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44 </help>
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45
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46 <citations>
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47 <citation type="doi">10.1101/gr.129684.111</citation>
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48 </citations>
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49 </tool>
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50
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51
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