Snake.config.json

{
    "sample"        : "D2Rfb",


    "mosaicatcher"  : "/g/korbel/meiers/tools/mosaicatcher/mosaicatcher/build/mosaicatcher",
    "plot_script"   : "/g/korbel/meiers/tools/mosaicatcher/mosaicatcher/R/qc.R",
    "sv_plot_script": "/g/korbel/meiers/tools/mosaicatcher/mosaicatcher/R/svs.R",
    "sce_script"    : "/g/korbel/meiers/tools/mosaicatcher/strandsequtils/sce_utils/SCE.R",
    "samtools"      : "module load SAMtools && samtools",
    "class_script"  : "finalCall_cmd.R",
    "class_dir"     : "/g/korbel/meiers/tools/mosaicatcher/strandsequtils/maryamCode",


    "exclude_file"  : "/g/korbel/meiers/tools/mosaicatcher/mosaicatcher/data/exclude/hg19.exclude",
    "variable_bins" : {
        "50000"     : "utils/variable_bins.GRCh38.50kb.bed",
        "100000"    : "utils/variable_bins.GRCh38.100kb.bed"
    },

    "bp_density"    : {
        "few"       : 0.1,
        "medium"    : 0.33,
        "many"      : 0.9
    }
}