config.json

{
    "java_cmd": "java -Xmx80G -jar",
    "gatk_path":"/nas/is1/bin/GATK/3.2-2/GenomeAnalysisTK.jar",
    "references": {
        "genome": "/nas/is1/reference/human/g1k_v37/human_g1k_v37.fasta"
    },
    "snpeff": {
        "path":
            "snpEff/snpEff.jar",
        "config":
            "snpEff/snpEff.config"
    },
    "samples": 
        ["NA12878","NA12891","NA12892"]
    ,
    "ped": "CEU.ped",
    "units": {
        "A":
            ["path/to/A_R1.fastq.gz", "path/to/A_R2.fastq.gz"],
        "B":
            ["path/to/B.fastq.gz"]
    },
    "known_variants": {
        "dbsnp": "00-All.vcf",
        "hapmap": "gatk_resources/hapmap_3.3.b37.vcf",
        "g1k": "gatk_resources/1000G_phase1.snps.high_confidence.b37.vcf",
        "omni": "gatk_resources/1000G_omni2.5.b37.vcf",
        "mills": "gatk_resources/Mills_and_1000G_gold_standard.indels.b37.vcf"
    },
    "platform": "Illumina",
    "heterozygosity": 0.001,
    "indel_heterozygosity": 1.25E-4,
    "range": "20",
    "filter": "hard"
}