modules/svtk_standardize

Groovy Map containing tool parameters. MUST follow the structure/keywords below and be provided via modules.config. Parameters must be set between quotes.

{  
  [  
    "args": "",  
    "caller": "delly" // Should be either delly, lumpy, manta, wham or melt  
  ]  
}  

{  
  [  
    "args": "",  
    "caller": "delly" // Should be either delly, lumpy, manta, wham or melt  
  ]  
}  

Groovy Map containing sample information
e.g. [ id:‘test’, single_end

A gzipped VCF file to be standardized

Optional fasta index file that specifies the contigs to be used in the VCF header (defaults to all contigs of GRCh37)