{
    "meta":{
        "name"          : "PGx - Germ Line - Customized parameters",
        "configuration" : "PGx_germline_low_stringency",
        "ts_version"    : "5.0",
        "compatibility" : {
          "chip"        : ["520","530","pgm"],
          "library"     : ["ampliseq"],
          "frequency"   : ["germline"],
          "stringency"  : ["low"]
        },
	"tvcargs"	: "tvc --use-input-allele-only"
    },
    "torrent_variant_caller":{

        "data_quality_stringency":6.5,
        "hp_max_length":10,
        "filter_unusual_predictions":0.7,
        "filter_insertion_predictions": 0.4,
        "filter_deletion_predictions": 0.2,
        "indel_as_hpindel": 0,

        "snp_min_cov_each_strand":0,
        "snp_min_variant_score":10.0,
        "snp_min_allele_freq":0.10,
        "snp_min_coverage":6,
        "snp_strand_bias":0.95,
        "snp_strand_bias_pval":1.0,

        "mnp_min_cov_each_strand":0,
        "mnp_min_variant_score":10.0,
        "mnp_min_allele_freq":0.10,
        "mnp_min_coverage":6,
        "mnp_strand_bias":0.95,
        "mnp_strand_bias_pval":1.0,

        "indel_min_cov_each_strand":5,
        "indel_min_variant_score":10.0,
        "indel_min_allele_freq":0.10,
        "indel_min_coverage":15,
        "indel_strand_bias":0.85,
        "indel_strand_bias_pval":1.0,

        "hotspot_min_cov_each_strand":3,
        "hotspot_min_variant_score":4.0,
        "hotspot_min_allele_freq":0.10,
        "hotspot_min_coverage":6,
        "hotspot_strand_bias":0.98,
        "hotspot_strand_bias_pval":0.01,

        "downsample_to_coverage":4000,
        "outlier_probability":0.01,
        "do_snp_realignment":1,
        "do_mnp_realignment":1,
        "realignment_threshold":1,

        "use_position_bias":0,
        "position_bias":0.75,
        "position_bias_pval":0.05,
        "position_bias_ref_fraction":0.05,

        "prediction_precision":1.0,
        "heavy_tailed":3,
        "suppress_recalibration":0,
        "process_input_positions_only": 1
    },
    "long_indel_assembler":{
        "kmer_len":19,
        "min_var_count":5,
        "short_suffix_match":5,
        "min_indel_size":4,
        "max_hp_length":8,
        "min_var_freq":0.15,
        "relative_strand_bias":0.8,
        "output_mnv":0
    },
    "freebayes":{
        "allow_indels":1,
        "allow_snps":1,
        "allow_mnps":1,
        "allow_complex":0,
        "min_mapping_qv":4,
        "read_snp_limit":10,
        "read_max_mismatch_fraction":1.0,
        "gen_min_alt_allele_freq":0.15,
        "gen_min_indel_alt_allele_freq":0.15,
        "gen_min_coverage":10
    }
}
