Mercurial > repos > p.lucas > varscan_readcount

comparison varscan_readcount.xml @ 12:0179feb477d7 draft default tip

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author p.lucas
date Thu, 10 Feb 2022 12:46:44 +0000
parents cad99097cdc2
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11:cad99097cdc2 12:0179feb477d7
14 <outputs> 14 <outputs>
15 <data name="output" format="vcf"/> 15 <data name="output" format="vcf"/>
16 </outputs> 16 </outputs>
17 <help> 17 <help>
18 USAGE: java -jar VarScan.jar readcounts pileup_file OPTIONS 18 USAGE: java -jar VarScan.jar readcounts pileup_file OPTIONS
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19 OPTIONS: 20 OPTIONS:
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20 --output-file Output file to contain the readcounts 22 --output-file Output file to contain the readcounts
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21 --min-coverage Minimum read depth at a position to make a call (default: 1) 24 --min-coverage Minimum read depth at a position to make a call (default: 1)
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22 --min-base-qual Minimum base quality at a position to count a read (default: 20) 26 --min-base-qual Minimum base quality at a position to count a read (default: 20)
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23 </help> 28 </help>
24 </tool> 29 </tool>