gistfile1.json

{ "pluginconfig" : 
  	{
		    "torrent_variant_caller":{
		        "downsample_to_coverage":2000,
		        "min_indel_count_for_genotyping":5,
		        "min_mapping_quality_score":4,
		        "min_allele_frequency":0.2,
		        "hp_low_stringency":0,
		        "hp_min_cov_each_strand":3,
		        "hp_stb_fpe_min_coverage":30,
		        "hp_stb_max_avg_peak_srand_distance":40,
		        "hp_stb_max_two_peaks_relative_bias":0.8,
		        "hp_max_single_peak_std_23":18,
		        "hp_max_single_peak_std_increment":5,
		        "fpe_max_peak_deviation":31,
		        "hp_max_length":9,
		        "info_vcf":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
		    },
		    "filter_indels":{
		        "min_bayesian_score":2.5,
		        "min_var_freq":0.199,
		        "bay_score_minlen":11,
		        "variant_strand_bias":0.9
		    },
		    "FreeBayes":{
		        "allowIndels":0,
		        "allowMNPs":0,
		        "allowSNPs":0,
		        "targets":"",
		        "leftAlignIndels":1,
		        "useBestNAlleles":2,
		        "forceRefAllele":1,
		        "onlyUseInputAlleles":1,
		        "MQL0":4,
		        "BQL0":4,
		        "RMU":10,
		        "readMaxMismatchFraction":1.0
		    }
		}
}