{
    "meta":{
        "name"          : "OCPv1i3 Panel - PGM - Somatic - Low Stringency",
        "tooltip"       : "Panel-specific parameters optimized for Oncomine Cancer Research AmpliSeq Panel",
        "configuration" : "ocp_somatic_lowstringency_pgm",
        "ts_version"    : "5.0",
        "compatibility" : {
          "chip"        : ["520","530","pgm"],
          "library"     : ["ampliseq"],
          "frequency"   : ["somatic"],
          "stringency"  : ["low"],
          "panel"       : true
        }
    },
    "torrent_variant_caller":{

        "data_quality_stringency":6.5,
        "hp_max_length":8,
        "filter_unusual_predictions":0.3,
        "filter_insertion_predictions": 0.2,
        "filter_deletion_predictions": 0.2,
        "indel_as_hpindel": 0,

        "snp_min_cov_each_strand":0,
        "snp_min_variant_score":6,
        "snp_min_allele_freq":0.04,
        "snp_min_coverage":15,
        "snp_strand_bias":0.96,
         "snp_strand_bias_pval":0.01,

        "mnp_min_cov_each_strand":0,
        "mnp_min_variant_score":400,
        "mnp_min_allele_freq":0.04,
        "mnp_min_coverage":15,
        "mnp_strand_bias":0.96,
        "mnp_strand_bias_pval":0.01,

        "indel_min_cov_each_strand":2,
        "indel_min_variant_score":20,
        "indel_min_allele_freq":0.07,
        "indel_min_coverage":15,
        "indel_strand_bias":0.90,
        "indel_strand_bias_pval":1.0,

        "hotspot_min_cov_each_strand":2,
        "hotspot_min_variant_score":8,
        "hotspot_min_allele_freq":0.03,
        "hotspot_min_coverage":15,
        "hotspot_strand_bias":0.96,
        "hotspot_strand_bias_pval":1.0,

        "downsample_to_coverage":2000,
        "outlier_probability":0.005,
        "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":1.0,
        "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":0.03,
        "gen_min_indel_alt_allele_freq":0.07,
        "gen_min_coverage":50
    },
    "cnvtools":{
        "trans_prob":-4.0,
        "trans_prob_gap":-4.0,
        "force_gene":1,
        "handle_pool":1,
        "trans_prob_gap_decay":0.00000057,
        "application_type":"Somatic",
        "from_ploidy":0.0,
        "to_ploidy":100.0,
        "ploidy_increment":0.1,
        "max_fold_trans_prob_ratio_gap":10
    }
}
