SYNOPSIS

icages.pl (input_file) [options]

OPTIONS

• -h, --help
  print help message

• -m, --manual
  print manual message

• -t, --tumor (TEXT)
  name of column that contains tumor mutations in your vcf file (if you have multiple samples with tumor mutations, please use this option to select tumor mutations that you want to analyze)

• -g, --germline (TEXT)
  name of column that contains germline mutations in your vcf file (if you have multiple samples with germline mutations, please use this option to select germline mutations that you want to compare your tumor mutations against to generate somatic mutation profiles for the sample you want to analyze)

• -i, --id (TEXT)
  name of column that contains somatic mutations in your multiple sample vcf file with only somatic mutations (if you have multiple samples with tumor and germline mutations, please use -g and -t options instead)

• -s, --subtype (TEXT)
  subtype of the cancer, valid options include "ACC", "BLCA", "BRCA", "CESC", "CHOL", "ESCA", "GBM", "HNSC", "KICH", "KIRC", "KIRP", "LAML", "LGG", "LIHC", "LUSC", "OV", "PAAD", "PCPG", "PRAD", "SARC", "SKCM", "STAD", "TGCT", "TGCA", "THYM", "UCEC", "UCS", "UVM"

• --logdir
  directory for log files generated by iCAGES

• --tempdir (TEXT)
  directory for temporary files generated by iCAGES

• --outputdir (TEXT)
  directory for output files generated by iCAGES

• -p, --prefix (TEXT)
  prefix of all files generated by iCAGES

• -b, --bed (TEXT)
  additional bed file specifying the location of structural variations in the sample. Note that if you only have bed file for the patient of your interest, please use it as input file directly without using -b option, with the command icages.pl input.bed

• --buildver (TEXT)
  reference genome version, valid options include "hg19", "hg38" and "hg18"

• -e, --expression (TEXT)
  bed file describing gene expression patterns, the columns are chromosome, start, end, log fold changes

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