{
    "reference_file"  :  "/hpc/hub_oudenaarden/group_references/ensembl/97/mus_musculus/SNP_MASKED.fa",
    "counting_min_mq" : 30,
    "counting_bin_sizes": [250_000],
    "counting_sliding_window_increments":[250_000],
    "alleles": "/hpc/hub_oudenaarden/group_references/variants/mgp.v5.merged.snps_all.dbSNP142.vcf.gz",
    "allele_samples": "C57BL_10J,CAST_EiJ",
    "mapper":"bowtie2"
}