{
    "reference_file"  :  "/hpc/hub_oudenaarden/group_references/ensembl/97/mus_musculus/SNP_MASKED.fa",
    "reference_file_for_mapper" : "/hpc/hub_oudenaarden/group_references/ensembl/97/mus_musculus/SNP_MASKED.fa",
    "mapfile" : "/hpc/hub_oudenaarden/group_references/ensembl/97/mus_musculus/simulated_CATG_single_69.mapability.safe.bgzf",
    "molecule_threshold": 10000,
    "counting_min_mq" : 30,
    "counting_bin_sizes": [500_000, 250_000, 1_000_000],
    "counting_sliding_window_increments":[250_000],
    "alleles": "none",
    "allele_samples": "none",
    "mapper":"bwa"
}