radia.template

{
    "tumor" : {
        "class" : "File",
        "path" : "</full/file/path>"         # Required file; replace '</full/file/path>' with full path to tumor DNA BAM file [e.g., /my/path/to/tumor.bam]
    },
    "normal" : {
        "class" : "File",
        "path" : "</full/file/path>"         # Required file; replace '</full/file/path>' with full path to normal DNA BAM file [e.g., /my/path/to/normal.bam]
    },
    "reference" : {
        "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]
    },
    "dnaNormalBaseQual" : null,             # Optional integer; minimum normal DNA base quality; 'null' defaults to '10'
    "dnaNormalDescription" : null,          # Optional string; description for normal sample in the VCF header; 'null' defaults to 'NormalDNASample'
    "dnaNormalFasta" : {
        "class" : "File:,
        "path" : null                      # Optional file; name of the FASTA file for the normal DNA BAM file
    },
    "dnaNormalMapQual" : null,              # Optional integer; minimum normal DNA mapping quality; 'null' defaults to '10'
    "dnaNormalMinAltBases" : null,          # Optional integer; minimum number of alternative normal DNA reads supporting a variant at a position; 'null' defaults to '2'
    "dnaNormalMinTotalBases" : null,        # Optional integer; minimum number of overall normal DNA reads covering a position; 'null' defaults to '4'
    "dnaTumorBaseQual" : null,              # Optional integer; minimum tumor DNA base quality; 'null' defaults to '10'
    "dnaTumorDescription" : null,           # Optional string; description for tumor sample in the VCF header; 'null' defaults to 'TumorDNASample'
    "dnaTumorFasta" : {
        "class" : "File",
        "path" : null                      # Optional file; name of the FASTA file for the tumor DNA BAM file
    },
    "dnaTumorMapQual" : null,               # Optional integer; minimum tumor DNA mapping quality; 'null' defaults to '10'
    "dnaTumorMinAltBases" : null,           # Optional integer; minimum number of alternative tumor DNA reads supporting a variant at a position; 'null' defaults to '2'
    "dnaTumorMinTotalBases" : null,         # Optional integer; minimum number of overall tumor DNA reads covering a position; 'null' defaults to '4'
    "rnaNormalBaiFilename" : {
        "class" : "File",
        "path" : null                      # Optional file; name of the normal RNA BAI file
    },
    "rnaNormalBaseQual" : null,             # Optional integer; minimum normal RNA base quality; 'null' defaults to '10'
    "rnaNormalDescription" : null,          # Optional string; description for normal sample in the VCF header; 'null' defaults to 'NormalRNASample'
    "rnaNormalFasta" : {
        "class" : "File",
        "path" : null                      # Optional file; name of the FASTA file for the normal RNA BAM file
    },
    "rnaNormalFilename" : {
        "class" : "File",
        "path" : null                      # Optional file; name of the normal RNA BAM file
    },
    "rnaNormalMapQual" : null,              # Optional integer; minimum normal RNA mapping quality; 'null' defaults to '10'
    "rnaNormalMinAltBases" : null,          # Optional integer; minimum number of alternative normal RNA reads supporting a variant at a position; 'null' defaults to '2'
    "rnaNormalMinTotalBases" : null,        # Optional integer; minimum number of overall normal RNA reads covering a position; 'null' defaults to '4'
    "rnaTumorBaiFilename" : {
        "class" : "File",
        "path" : null                      # Optional file; name of the tumor RNA BAI file
    },
    "rnaTumorBaseQual" : null,            # Optional integer; minimum tumor RNA base quality; 'null' defaults to '10'
    "rnaTumorDescription" : null,           # Optional string; description for tumor sample in the VCF header; 'null' defaults to 'TumorRNASample'
    "rnaTumorFasta" : {
        "class" : "File",
        "path" : null                      # Optional file; name of the tumor RNA BAI file
    },
    "rnaTumorFilename" : {
        "class" : "File",
        "path" : null                      # Optional file; name of the tumor RNA BAM file
    },
    "rnaTumorMapQual" : null,               # Optional integer; minimum tumor RNA mapping quality; 'null' defaults to '10'
    "rnaTumorMinAltBases" : null,           # Optional integer; minimum number of alternative tumor RNA reads supporting a variant at a position; 'null' defaults to '2'
    "rnaTumorMinTotalBases" : null,         # Optional integer; minimum number of overall tumor RNA reads covering a position; 'null' defaults to '4'
    "genotypeMinDepth" : null,              # Optional integer; minimum number of bases required for the genotype; 'null' defaults to '2'
    "genotypeMinPct" : null,                # Optional float; minimum percentage of reads required for the genotype; 'null' defaults to '0.10'
    "gzip" : null,                          # Optional boolean; replace 'null' with 'true' to obtain gzip-compressed final VCF; 'null' defaults to 'false'
    "log" : null,                           # Optional string; logging level options include DEBUG, INFO, WARNING, ERROR, or CRITICAL; 'null' defaults to 'WARNING'
    "logFilename" : null,                   # Optional string; name for the log file; 'null' defaults to STDOUT
    "no_clean" : null,                      # Optional boolean; replace 'null' with 'true' to prevent removal of intermediate files; 'null' defaults to 'false'
    "number_of_procs" : null,               # Optional integer; number of CPUs to use; 'null' defaults to '1'
    "out_vcf" : null,                       # Optional string; name of the output VCF; 'null' defaults to 'radia.vcf'
    "outputDir" : null,                     # Optional string; full path to directory where temporary and final filtered outputs should be stored [e.g. /my/path/to/output/]; 'null' defaults to './'
    "workdir" : null,                       # Optional string; full path to working directory to use [e.g., /my/path/to/wrkdir/]; 'null' defaults to './'
    "refId" : null,                         # Optional string; short ID for reference (used in the sample VCF meta tag) [e.g., GRCh37]
    "refUrl" : null,                        # Optional string; URL link to reference (used in the sample VCF meta tag)
    "refFilename" : null,                   # Optional string; full path to the reference file (used in the sample VCF meta tag) [e.g., /my/path/to/genome.fa.gz]
    "dataSource" : null,                    # Optional string; source of the data (used in the sample VCF meta tag)
    "sequencingPlatform" : null,            # Optional string; one-word description of sequencing platform (used in the sample VCF meta tag) [e.g. illumina]
    "patientId" : null,                     # Optional string; unique patient ID to add to the SAMPLE and INDIVIDUAL tags in the final VCF header; 'null' defaults to 'myPatient'
    "batchSize" : null,                     # Optional integer; size of the samtools selections that are loaded into memory at one time; 'null' defaults to '250000000' 
    "disease" : null,                       # Optional string; disease abbreviation to be used in the header [e.g., BRCA]
    "statsDir" : null,                      # Optional string; full path to directory where some basic stats can be output [e.g., /my/path/to/stats/]
    "useChrPrefix" : null                 # Optional boolean; replace 'null' with 'true' to use 'chr' prefix in samtools command for all BAMs; 'null' defaults to 'false'
}