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

    "reference"     : "/MMCI/TM/scratch/ref/GRCh38_no_alt_analysis_set/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna",
    "mosaicatcher"  : "/MMCI/TM/scratch/strandseq/mosaicatcher-builds/git/build/mosaic",
    "plot_script"   : "/MMCI/TM/scratch/strandseq/mosaicatcher-builds/git/R/qc.R",
    "samtools"      : "samtools",
    "bcftools"      : "bcftools",

    "snv_sites_to_genotype": "/MMCI/TM/scratch/MosaiCatcher_data/RPE1_cell_lines/Compare_SNVsCalls/GRCh38_1000G_variableSites/ALL.chr1-22plusX_GRCh38_sites.20170504.renamedCHR.vcf.gz",

    "snv_calls"     : {},

    "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"       : 0.2,
        "medium"    : 0.4,
        "many"      : 0.6
    },

    "paired_end"    : true,

    "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,

    "ground_truth_clonal" : {
        "RPE-BM510" : "/MMCI/TM/scratch/strandseq/input-data/ground_truth/RPE-BM510_manual/clonal-events.tsv"
    },

    "ground_truth_single_cell" : {
        "RPE-BM510" : "/MMCI/TM/scratch/strandseq/input-data/ground_truth/RPE-BM510_manual/single-cell-events.tsv"
    }
}