vcf2vcf.template

{
    "inputVCF" : {
        "class" : "File",
        "path": "</full/file/path>"         # Required file; replace '</full/file/path>' with full path to input VCF [e.g., /my/path/to/input.vcf]
    },
    "refFasta" : {
        "class" : "File",
        "path": "</full/file/path>"         # Required file; replace '</full/file/path>' with full path to reference FASTA [e.g., /my/path/to/genome.fa.gz]
    },
    "outputVCF" : null,                     # Optional string: replace 'null' with output file name; 'null' defaults to 'output.vcf'
    "addFilters" : "false",                   # Optional boolean; replace 'false' with 'true' to add some extra tags under the FILTER column of the MAF; 'null' defaults to 'true'
    "vcfNormalID" : null,                   # Optional string; matched normal ID used in the input VCF; 'null' defaults to 'NORMAL'
    "vcfTumorID" : null,                    # Optional string; tumor ID used in the input VCF; 'null' defaults to 'TUMOR'
    "newNormalID" : null,                   # Optional string; matched normal ID to use in the new VCF; 'null' defaults to 'vcfNormalID' setting
    "newTumorID" : null                    # Optional string; tumor ID to use in the new VCF; 'null' defaults to 'vcfTumorID' setting
}