config.json

{
    # Next three lines are making this: /scr/k41san/genomes/GRCh38/GRCh38.ver2.fa
    "REFERENCE": "/scr/k41san/genomes/", #Path to your reference folder
    "GENOME": "GRCh38", #Folder name which your genome is there
    "NAME": ".ver2", #Extension of your GenomeName (Look at the above example)
    "OTHERSCRIPT": "scripts", # Where can I find other scripts
    "POPULATION": { # All of your population
        "A": "PopA",
        "B": "PopB"
    },
    "INDIVIDUALS":{ 
        "A": 
           ["PopA_Ind1","PopA_Ind1","PopA_Ind2","PopA_Ind2","PopA_Ind3","PopA_Ind3"],
        "B": 
           ["PopB_Ind1","PopB_Ind1","PopB_Ind2","PopB_Ind2","PopB_Ind3","PopB_Ind3"]
    },
    "MAPPER": "/usr/local/bin/bwa-0.7.12/bwa" ,
    "SAMTOOLS": "/usr/local/bin/samtools-1.3.1/samtools" ,
    "PICARD": "/usr/local/bin/picard-1.140/dist/picard.jar",
    "JAVA_1_8": "/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.121-0.b13.el7_3.x86_64/jre/bin/java",
    "WHERE" : "/homes/biertruck/amin/Project/SNPCallingComp/Data" 
    # Other tools also must be configured here
}