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",
    "plot_segments" : "/g/korbel/meiers/tools/mosaicatcher/mosaicatcher/R/plot_segments.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"    : 0.25,
        "many"      : 0.5
    },

    "paired_end"    : false,

    "simulation_min_vaf" : 0.01,
    "simulation_max_vaf" : 1.0,
    "simulation_neg_binom_p" : {
        "50000" : 0.4,
        "100000" : 0.3,
        "500000" : 0.1
    },
    "simulation_min_reads_per_library" :  500000,
    "simulation_max_reads_per_library" : 1000000,
    "simulation_window_sizes" : [50000, 100000],
    "simulation_cell_count" : 100,
    "simulation_alpha" : 0.02,

    "genome_size" : 3e9

}