{
    "meta":{
        "name"          : "TargetSeq - Proton - Germ Line - Low Stringency",
        "tooltip"       : "Parameter settings optimized for high frequency variants and minimum false negatives on TargetSeq libraries and Proton chips",
        "configuration" : "germline_low_stringency_targetseq",
        "ts_version"    : "5.0",
        "compatibility" : {
          "chip"        : ["540","proton_p1"],
          "library"     : ["targetseq","wholegenome"],
          "frequency"   : ["germline"],
          "stringency"  : ["low"]

        }
    },
    "torrent_variant_caller":{

        "data_quality_stringency":5.0,
        "hp_max_length":8,
        "filter_unusual_predictions":0.25,
        "filter_insertion_predictions": 0.2,
        "filter_deletion_predictions": 0.2,
        "indel_as_hpindel": 1,

        "snp_min_cov_each_strand":0,
        "snp_min_variant_score":15.0,
        "snp_min_allele_freq":0.10,
        "snp_min_coverage":5,
        "snp_strand_bias":0.98,
        "snp_strand_bias_pval":0.01,

        "mnp_min_cov_each_strand":0,
        "mnp_min_variant_score":60.0,
        "mnp_min_allele_freq":0.10,
        "mnp_min_coverage":5,
        "mnp_strand_bias":0.98,
        "mnp_strand_bias_pval":0.01,

        "indel_min_cov_each_strand":5,
        "indel_min_variant_score":20.0,
        "indel_min_allele_freq":0.25,
        "indel_min_coverage":10,
        "indel_strand_bias":0.9,
        "indel_strand_bias_pval":1.0,

        "hotspot_min_cov_each_strand":3,
        "hotspot_min_variant_score":10.0,
        "hotspot_min_allele_freq":0.10,
        "hotspot_min_coverage":6,
        "hotspot_strand_bias":0.95,
        "hotspot_strand_bias_pval":1.0,

        "downsample_to_coverage":400,
        "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,

        "sse_prob_threshold":0.2,
        "prediction_precision":1.0,
        "heavy_tailed":3,
        "suppress_recalibration":0
    },
    "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":0.1,
        "gen_min_indel_alt_allele_freq":0.15,
        "gen_min_coverage":5
    }
}
