{
    "genotype": "../02plinkb",
    "pedigree": "../05others/pedigree.txt",
    "selection_index": "100 - 0.2 * T1 + 0.8 * T2",
    "threads": 16,
    "genetic_progress": [],
    "breeding_value_index": "-0.2 * T1 + 0.8 * T2",
    "auto_optimization": true,
    "quality_control_plan": {
        "genotype_quality_control":{
            "filter": "F1 == 'Male'",
            "filter_geno": 0.1,
            "filter_mind": 0.1,
            "filter_maf": 0.05,
            "filter_hwe": 0.001
        },
        "pedigree_quality_control":{
            "standard_ID": false,
            "candidate_sire_file": [],
            "candidate_dam_file": [],
            "exclude_threshold": 0.1, 
            "assign_threshold": 0.05
        },
        "phenotype_quality_control":[
            {
                "job_name": "Data_Quality_Control_Demo",
                "sample_info": "../05others/phenotype.txt",
                "repeated_records": false,
                "multi_trait": true,
                "filter": "F1 == 'Male'",
                "job_traits": [
                    {
                        "traits": "T1",
                        "definition": "T1",
                        "range": []
                    },
                    {
                        "traits": "T2",
                        "definition": "T2",
                        "range": []
                    }
                ]
            }
        ]
    },
    "breeding_plan":[
        {
            "job_name": "EBV_Model_Demo",
            "sample_info": "../05others/phenotype.txt",
            "repeated_records": false,
            "multi_trait": true,
            "vc_vars": [],
            "vc_covars": [],
            "random_ratio": 0.05,
            "job_traits": [
                {
                    "traits": "T1",
                    "covariates": [],
                    "fixed_effects": ["F1", "F2"],
                    "random_effects": ["R1"]
                },
                {
                    "traits": "T2",
                    "covariates": [],
                    "fixed_effects": ["F1", "F2"],
                    "random_effects": ["R1"]
                }
            ]
        }
    ]
}