pindel-somatic.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]
    },
    "centromere" : {
        "class" : "File",
        "path" : "</full/file/path>"             # Required file; replace '</full/file/path>' with centromere location BED file [e.g., /my/path/to/centromere.bed]
    },
    "additional_mismatch" : null,               # Optional integer; only map part of a read to the reference genome if there are no other candidate positions with no more than this number of mismatches position (larger values are more accurate but less sensitive); 'null' defaults to '1'
    "outputRawFile" : null,                     # Optional string; name of raw output file; 'null' defaults to 'pindel.raw'
    "outputSomaticVcfFile" : null,              # Optional string; name of somatic VCF output file; 'null' defaults to 'pindel_somatic.vcf'
    "outputVcfFile" : null,                     # Optional string; name of full VCF output file; 'null' defaults to 'pindel.vcf'
    "procs" : null,                             # Optional integer; number of threads to run Pindel; 'null' defaults to '2'
    "balance_cutoff" : null,                    # Optional integer; number of bases of an SV above which a more stringent filter is applied; 'null' defaults to '100'
    "max_range_index" : null,                   # Optional integer; maximum size of structural variations to be detected; 'null' defaults to '4'
    "maximum_allowed_mismatch_rate" : null,     # Optional float; only reads with fewer mismatches with the reference genome than this fraction will be considered; 'null' defaults to '0.02'
    "min_inversion_size" : null,                # Optional integer; only report inversions greater than this number of bases; 'null' defaults to '50'
    "min_num_matched_bases" : null,             # Optional integer; only consider reads as evidence if they map with more than this number of bases to the reference; 'null' defaults to '30'
    "min_perfect_match_around_BP" : null,       # Optional integer; there should at least be this number of perfectly matching bases between read and reference where the read is split into two; 'null' defaults to '3'
    "minimum_support_for_event" : null,         # Optional integer; minimum supporting reads to call an event; 'null' defaults to '1'
    "normal_insert_size" : null,                # Optional integer; insert size of normal reads
    "referenceName" : null,                     # Optional string; Short name for reference file; 'null' defaults to 'HG19'
    "report_breakpoints" : null,                # Optional boolean; replace 'null' with 'true' to report breakpoints; 'null' defaults to 'false'
    "report_duplications" : null,               # Optional boolean; replace 'null' with 'true' to report duplications; 'null' defaults to 'false'
    "report_inversions" : null,                 # Optional boolean; replace 'null' with 'true' to report inversions; 'null' defaults to 'false'
    "report_long_insertions" : null,            # Optional boolean; replace 'null' with 'true' to enable report long insertions; 'null' defaults to 'false'
    "report_only_close_mapped_reads" : null,    # Optional boolean; replace 'null' with 'true' to enable report only closely mapped reads; 'null' defaults to 'false'
    "sensitivity" : null,                       # Optional float; 'null' defaults to '0.95'
    "sequencing_error_rate" : null,             # Optional float; 'null' defaults to '0.01'
    "somatic_cov" : null,                       # Optional integer; 'null' defaults to '20'
    "somatic_hom" : null,                       # Optional integer; 'null' defaults to '6'
    "somatic_vaf" : null,                       # Optional float; 'null' defaults to '0.08'
    "tumor_insert_size" : null,                 # Optional integer; insert size of tumor reads
    "window_size" : null                       # Optional float; 'null' defaults to '5.0'
}