config.json

{
    "references": {
        "fasta": "genome/mm10.fa",
        "snp": "snp/",
        "assembly": "mm10",
        "chroms": "/oasis/tscc/scratch/lpatel/00_ref/mm10.chrom.sizes"
    },
    "units": {
        "test": ""
    },
    "bins": ["b6", "cast", "homo", "amb", "un"],
    "input_format": {
        "suffix": ".bz2",
        "command": "bzcat"
    },
    "software": {
        "bwa": "bwa",
        "samtools": "samtools",
        "juicertools": "/home/lpatel/software/juicertools/juicer_tools_1.22.01.jar",
        "pairtools": "pairtools",
        "cooler": "cooler",
        "hic2cool": "hic2cool",
        "python2": "~/software/miniconda3/envs/py2/bin/python",
        "java": "/bin/java"
    },
    "scripts": {
        "combine_read_pairs": "scripts/combine_reads_wasp_5-02-16.pl",
        "filt_chmeric1": "scripts/filter_five_end_wasp_1.pl",
        "filt_chmeric2": "scripts/filter_five_end_wasp_2.pl",
        "find_snp": "scripts/find_intersecting_snps_YQ.py",
        "compare": "scripts/filter_remapped_reads_q10.py",
        "haplotype": "scripts/assign_haplotypes.py",
        "split": "scripts/split_haplotypes.py",
        "count": "scripts/count_distances.py",
        "pairing": "scripts/homolog_pairing.py"
    },
    "threads": {
          "bwa": "4"
    },
    "map_quality" : "10",
    "platform": "Illumina"
}