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SeqShop: Analysis of Structural Variation Practical, December 2014 (view source)

Revision as of 12:25, 10 December 2014

128 bytes added ,  12:25, 10 December 2014
→‎Command Line Usage of GenomeSTRiP pipeline
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  perl $GC/bin/genomestrip.pl  
 
  perl $GC/bin/genomestrip.pl  
    +
<div class="mw-collapsible" style="width:800px">
 +
''View Results''
 +
<div class="mw-collapsible-content" style="width:800px">
 
  ERROR: One of command options among --run-metadata, --run-discovery, --run-genotype, --run-thirdparty must be specified
 
  ERROR: One of command options among --run-metadata, --run-discovery, --run-genotype, --run-thirdparty must be specified
 
  ERROR: Missing required option, outdir
 
  ERROR: Missing required option, outdir
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     /net/seqshop-server/home/mktrost/seqshop/gotcloud/bin/genomestrip.pl
 
     /net/seqshop-server/home/mktrost/seqshop/gotcloud/bin/genomestrip.pl
 
     [options]
 
     [options]
−
 
+
 
     Help Options:
 
     Help Options:
 
       -help                Print out brief help message [OFF]
 
       -help                Print out brief help message [OFF]
 
       -man                Print the full documentation in man page style [OFF]
 
       -man                Print the full documentation in man page style [OFF]
−
 
+
 
     Command options:
 
     Command options:
 
       -run-metadata        Create metadata [OFF]
 
       -run-metadata        Create metadata [OFF]
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       -run-genotype        Run genotyping - requires to finish run-metadata and run-discovery [OFF]
 
       -run-genotype        Run genotyping - requires to finish run-metadata and run-discovery [OFF]
 
       -run-thirdparty      Run genotyping and filtering of third-party sites [OFF]
 
       -run-thirdparty      Run genotyping and filtering of third-party sites [OFF]
−
 
+
 
     Options for input/output data:
 
     Options for input/output data:
 
       -gotcloudroot|gcroot STRGotCloud Root Directory []
 
       -gotcloudroot|gcroot STRGotCloud Root Directory []
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       -genotype STR        Output directory to store --run-genotype results. Default is [OUT]/genotype/ []
 
       -genotype STR        Output directory to store --run-genotype results. Default is [OUT]/genotype/ []
 
       -thirdparty STR      Output directory to store --run-thirdparty results. Default is [OUT]/thirdparty/ []
 
       -thirdparty STR      Output directory to store --run-thirdparty results. Default is [OUT]/thirdparty/ []
−
 
+
 
     Advanced Options:
 
     Advanced Options:
 
       -tmp-dir STR        temporary directory to store temporary files. Default is [OUT]/tmp []
 
       -tmp-dir STR        temporary directory to store temporary files. Default is [OUT]/tmp []
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       -region STR          Region to focus on the variants []
 
       -region STR          Region to focus on the variants []
 
       -unit INT            Number of variants to be genotyped per parallel run [100]
 
       -unit INT            Number of variants to be genotyped per parallel run [100]
−
 
+
 
     Additional Inputs:
 
     Additional Inputs:
 
       -in-vcf STR          Input site VCF files used for --run-genotype or --run-thirdparty. For --run-thirdparty, this argument is required. For --run-genotype, default is [OUT]/discovery/discovery.vcf []
 
       -in-vcf STR          Input site VCF files used for --run-genotype or --run-thirdparty. For --run-thirdparty, this argument is required. For --run-genotype, default is [OUT]/discovery/discovery.vcf []
Retrieved from "http://genome.sph.umich.edu/wiki/Special:MobileDiff/12311"

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