Snake.config.json

{
    "chromosomes"   : ["chrX","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/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna",
    "mosaicatcher"  : "/g/korbel/meiers/tools/mosaicatcher/mosaicatcher_experimental/build/mosaicatcher",
    "plot_script"   : "/g/korbel/meiers/tools/mosaicatcher/mosaicatcher_experimental/R/qc.R",
    "sv_plot_script": "/g/korbel/meiers/tools/mosaicatcher/mosaicatcher_experimental/R/chrom.R",
    "norm_script"   : "/g/korbel/meiers/tools/mosaicatcher/mosaicatcher_experimental/R/norm.R",
    "samtools"      : "samtools",
    "bcftools"      : "bcftools",

    "snv_calls"     : {
        "C7_data"   : "/g/korbel2/StrandSeq/20180221_RPE_Data/regenSNVs_GRCh38sites_C7_chr1-22plusX.filtered.vcf.gz",
		"RPE-BM510" : "/g/korbel2/StrandSeq/20180221_RPE_Data/regenSNVs_GRCh38sites_BM510_chr1-22plusX.filtered.vcf.gz",
		"RPE1-WT"   : "/g/korbel2/StrandSeq/20180606_RPE1-WT/regenSNVs_GRCh38sites_RPEWTstrandS_chr1-22plusX.filtered.vcf.gz"
	},

    "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

}