Snake.config.json

{
    "chromosomes"   : ["chr1","chr2","chr3","chr4","chr5","chr6","chr7","chr8","chr9","chr10","chr11","chr12","chr13","chr14","chr15","chr16","chr17","chr18","chr19","chr20","chr21","chr22"],

    "reference"     : "/g/korbel/shared/datasets/refgenomes/human/hg19_chr1_22XYM.fa",
    "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"      : "samtools",
    "bcftools"      : "bcftools",

    "snv_calls"     : {},

    "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"
    },
    "R_reference"   : "BSgenome.Hsapiens.UCSC.hg38",

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