annotate freebayes.xml @ 3:213a3d6b579a

Change the tool dependecy definition
author greg <greg@bx.psu.edu>
date Fri, 13 Jul 2012 12:52:45 -0400
parents 838dd557c84c
children e54bb199a47b
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1 <?xml version="1.0"?>
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2 <tool id="freebayes" name="FreeBayes" version="0.0.2">
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3 <requirements>
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4 <requirement type="package" version="0.9.4_a46483351fd0196637614121868fb5c386612b55">freebayes</requirement>
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5 <requirement type="package" version="0.1.18">samtools</requirement>
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6 </requirements>
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7 <description> - Bayesian genetic variant detector</description>
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8 <command>
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9 ##set up input files
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10 #set $reference_fasta_filename = "localref.fa"
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11 #if str( $reference_source.reference_source_selector ) == "history":
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12 ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" &amp;&amp;
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13 samtools faidx "${reference_fasta_filename}" 2&gt;&amp;1 || echo "Error running samtools faidx for FreeBayes" &gt;&amp;2 &amp;&amp;
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14 #else:
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15 #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path )
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16 #end if
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17 #for $bam_count, $input_bam in enumerate( $reference_source.input_bams ):
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18 ln -s "${input_bam.input_bam}" "localbam_${bam_count}.bam" &amp;&amp;
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19 ln -s "${input_bam.input_bam.metadata.bam_index}" "localbam_${bam_count}.bam.bai" &amp;&amp;
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20 #end for
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21 ##finished setting up inputs
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22
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23 ##start FreeBayes commandline
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24 freebayes
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25 #for $bam_count, $input_bam in enumerate( $reference_source.input_bams ):
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26 --bam "localbam_${bam_count}.bam"
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27 #end for
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28 --fasta-reference "${reference_fasta_filename}"
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29
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30 ##outputs
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31 --vcf "${output_vcf}"
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32
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33 ##advanced options
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34 #if str( $options_type.options_type_selector ) == "advanced":
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35 ##additional outputs
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36 #if $options_type.output_trace_option:
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37 --trace "${output_trace}"
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38 #end if
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39 #if $options_type.output_failed_alleles_option:
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40 --failed-alleles "${output_failed_alleles_bed}"
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41 #end if
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42
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43 ##additional inputs
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44 #if str( $options_type.target_limit_type.target_limit_type_selector ) == "limit_by_target_file":
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45 --targets "${options_type.target_limit_type.input_target_bed}"
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46 #elif str( $options_type.target_limit_type.target_limit_type_selector ) == "limit_by_region":
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47 --region "${options_type.target_limit_type.region_chromosome}:${options_type.target_limit_type.region_start}..${options_type.target_limit_type.region_end}"
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48 #end if
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49 #if $options_type.input_sample_file:
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50 --samples "${options_type.input_sample_file}"
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51 #end if
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52 #if $options_type.input_populations_file:
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53 --populations "${options_type.input_populations_file}"
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54 #end if
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55 #if $options_type.input_cnv_map_bed:
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56 --cnv-map "${options_type.input_cnv_map_bed}"
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57 #end if
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58 #if str( $options_type.input_variant_type.input_variant_type_selector ) == "provide_vcf":
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59 --variant-input "${options_type.input_variant_type.input_variant_vcf}"
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60 ${options_type.input_variant_type.only_use_input_alleles}
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61 #end if
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62
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63 ##reporting
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64 #if str( $options_type.section_reporting_type.section_reporting_type_selector ) == "set":
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65 --pvar "${options_type.section_reporting_type.pvar}"
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66 ${options_type.section_reporting_type.show_reference_repeats}
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67 #end if
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68
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69 ##population model
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70 #if str( $options_type.section_population_model_type.section_population_model_type_selector ) == "set":
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71 --theta "${options_type.section_population_model_type.theta}"
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72 --ploidy "${options_type.section_population_model_type.ploidy}"
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73 ${options_type.section_population_model_type.pooled}
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74 #end if
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75
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76 ##reference allele
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77 #if str( $options_type.use_reference_allele_type.use_reference_allele_type_selector ) == "include_reference_allele":
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78 --use-reference-allele
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79 ${options_type.use_reference_allele_type.diploid_reference}
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80 --reference-quality "${options_type.use_reference_allele_type.reference_quality_mq},${options_type.use_reference_allele_type.reference_quality_bq}"
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81 #end if
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82
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83 ##allele scope
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84 #if str( $options_type.section_allele_scope_type.section_allele_scope_type_selector ) == "set":
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85 ${options_type.section_allele_scope_type.no_snps}
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86 ${options_type.section_allele_scope_type.no_indels}
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87 ${options_type.section_allele_scope_type.no_mnps}
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88 ${options_type.section_allele_scope_type.no_complex}
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89 --use-best-n-alleles "${options_type.section_allele_scope_type.use_best_n_alleles}"
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90 #if $options_type.section_allele_scope_type.max_complex_gap:
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91 --max-complex-gap "${options_type.section_allele_scope_type.max_complex_gap}"
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92 #end if
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93 #end if
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94
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95 ##indel realignment
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96 ${options_type.left_align_indels}
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97
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98 ##input filters
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99 #if str( $options_type.section_input_filters_type.section_input_filters_type_selector ) == "set":
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100 ${options_type.section_input_filters_type.use_duplicate_reads}
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101 #if str( $options_type.section_input_filters_type.no_filter_type.no_filter_type_selector ) == "apply_filters":
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102 --min-mapping-quality "${options_type.section_input_filters_type.no_filter_type.min_mapping_quality}"
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103 --min-base-quality "${options_type.section_input_filters_type.no_filter_type.min_base_quality}"
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104 --min-supporting-quality "${options_type.section_input_filters_type.no_filter_type.min_supporting_quality_mq},${options_type.section_input_filters_type.no_filter_type.min_supporting_quality_bq}"
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105 #else:
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106 --no-filters
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107 #end if
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108 --mismatch-base-quality-threshold "${options_type.section_input_filters_type.mismatch_base_quality_threshold}"
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109 #if $options_type.section_input_filters_type.read_mismatch_limit:
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110 --read-mismatch-limit "${options_type.section_input_filters_type.read_mismatch_limit}"
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111 #end if
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112 --read-max-mismatch-fraction "${options_type.section_input_filters_type.read_max_mismatch_fraction}"
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113 #if $options_type.section_input_filters_type.read_snp_limit:
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114 --read-snp-limit "${options_type.section_input_filters_type.read_snp_limit}"
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115 #end if
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116 #if $options_type.section_input_filters_type.read_indel_limit:
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117 --read-indel-limit "${options_type.section_input_filters_type.read_indel_limit}"
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118 #end if
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119 --indel-exclusion-window "${options_type.section_input_filters_type.indel_exclusion_window}"
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120 --min-alternate-fraction "${options_type.section_input_filters_type.min_alternate_fraction}"
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121 --min-alternate-count "${options_type.section_input_filters_type.min_alternate_count}"
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122 --min-alternate-qsum "${options_type.section_input_filters_type.min_alternate_qsum}"
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123 --min-alternate-total "${options_type.section_input_filters_type.min_alternate_total}"
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124 --min-coverage "${options_type.section_input_filters_type.min_coverage}"
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125 #end if
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126
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127 ##bayesian priors
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128 #if str( $options_type.section_bayesian_priors_type.section_bayesian_priors_type_selector ) == "set":
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129 ${options_type.section_bayesian_priors_type.no_ewens_priors}
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130 ${options_type.section_bayesian_priors_type.no_population_priors}
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131 ${options_type.section_bayesian_priors_type.hwe_priors}
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132 #end if
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133
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134 ##observation prior expectations
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135 #if str( $options_type.section_observation_prior_expectations_type.section_observation_prior_expectations_type_selector ) == "set":
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136 ${options_type.section_observation_prior_expectations_type.binomial_obs_priors}
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137 ${options_type.section_observation_prior_expectations_type.allele_balance_priors}
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138 #end if
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139
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140 ##algorithmic features
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141 #if str( $options_type.section_algorithmic_features_type.section_algorithmic_features_type_selector ) == "set":
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142 --site-selection-max-iterations "${options_type.section_algorithmic_features_type.site_selection_max_iterations}"
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143 --genotyping-max-iterations "${options_type.section_algorithmic_features_type.genotyping_max_iterations}"
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144 --genotyping-max-banddepth "${options_type.section_algorithmic_features_type.genotyping_max_banddepth}"
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145 --posterior-integration-limits "${options_type.section_algorithmic_features_type.posterior_integration_limits_n},${options_type.section_algorithmic_features_type.posterior_integration_limits_m}"
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146 ${options_type.section_algorithmic_features_type.no_permute}
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147 ${options_type.section_algorithmic_features_type.exclude_unobserved_genotypes}
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148 #if $options_type.section_algorithmic_features_type.genotype_variant_threshold:
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149 --genotype-variant-threshold "${options_type.section_algorithmic_features_type.genotype_variant_threshold}"
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150 #end if
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151 ${options_type.section_algorithmic_features_type.use_mapping_quality}
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152 --read-dependence-factor "${options_type.section_algorithmic_features_type.read_dependence_factor}"
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153 ${options_type.section_algorithmic_features_type.no_marginals}
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154 #end if
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155
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156 #end if
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157 </command>
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158 <inputs>
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159 <conditional name="reference_source">
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160 <param name="reference_source_selector" type="select" label="Choose the source for the reference list">
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161 <option value="cached">Locally cached</option>
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162 <option value="history">History</option>
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163 </param>
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164 <when value="cached">
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165 <repeat name="input_bams" title="Sample BAM file" min="1">
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166 <param name="input_bam" type="data" format="bam" label="BAM file">
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167 <validator type="unspecified_build" />
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168 <validator type="dataset_metadata_in_data_table" table_name="sam_fa_indexes" metadata_name="dbkey" metadata_column="value" message="Sequences are not currently available for the specified build." />
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169 </param>
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170 </repeat>
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171 <param name="ref_file" type="select" label="Using reference genome">
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172 <options from_data_table="sam_fa_indexes">
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173 <!-- <filter type="sam_fa_indexes" key="dbkey" ref="input_bam" column="value"/> does not yet work in a repeat...-->
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174 </options>
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175 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
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176 </param>
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177 </when>
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178 <when value="history"> <!-- FIX ME!!!! -->
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179 <repeat name="input_bams" title="Sample BAM file" min="1">
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180 <param name="input_bam" type="data" format="bam" label="BAM file" />
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181 </repeat>
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182 <param name="ref_file" type="data" format="fasta" label="Using reference file" />
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183 </when>
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184 </conditional>
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185
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186 <conditional name="options_type">
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187 <param name="options_type_selector" type="select" label="Basic or Advanced options">
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188 <option value="basic" selected="True">Basic</option>
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189 <option value="advanced">Advanced</option>
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190 </param>
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191 <when value="basic">
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192 <!-- Do nothing here -->
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193 </when>
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194 <when value="advanced">
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195
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196 <!-- output -->
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197 <param name="output_failed_alleles_option" type="boolean" truevalue="--failed-alleles" falsevalue="" checked="False" label="Write out failed alleles file" />
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198 <param name="output_trace_option" type="boolean" truevalue="--trace" falsevalue="" checked="False" label="Write out algorithm trace file" />
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199
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200
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201 <!-- input -->
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202 <conditional name="target_limit_type">
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203 <param name="target_limit_type_selector" type="select" label="Limit analysis to listed targets">
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204 <option value="do_not_limit" selected="True">Do not limit</option>
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205 <option value="limit_by_target_file">Limit by target file</option>
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206 <option value="limit_by_region">Limit to region</option>
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207 </param>
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208 <when value="do_not_limit">
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209 <!-- Do nothing here -->
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210 </when>
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211 <when value="limit_by_target_file">
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212 <param name="input_target_bed" type="data" format="bed" label="Limit analysis to targets listed in the BED-format FILE." />
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213 </when>
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214 <when value="limit_by_region">
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215 <param name="region_chromosome" type="text" label="Region Chromosome" value="" /> <!--only once? -->
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216 <param name="region_start" type="integer" label="Region Start" value="" />
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217 <param name="region_end" type="integer" label="Region End" value="" />
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218 </when>
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219 </conditional>
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220 <param name="input_sample_file" type="data" format="txt" label="Limit analysis to samples listed (one per line) in the FILE" optional="True" />
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221 <param name="input_populations_file" type="data" format="txt" label="Populations File" optional="True" />
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222 <param name="input_cnv_map_bed" type="data" format="bed" label="Read a copy number map from the BED file FILE" optional="True" />
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223 <conditional name="input_variant_type">
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224 <param name="input_variant_type_selector" type="select" label="Provide variants file">
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225 <option value="do_not_provide" selected="True">Do not provide</option>
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226 <option value="provide_vcf">Provide VCF file</option>
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227 </param>
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228 <when value="do_not_provide">
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229 <!-- Do nothing here -->
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230 </when>
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231 <when value="provide_vcf">
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232 <param name="input_variant_vcf" type="data" format="vcf" label="Use variants reported in VCF file as input to the algorithm" />
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233 <param name="only_use_input_alleles" type="boolean" truevalue="--only-use-input-alleles" falsevalue="" checked="False" label="Only provide variant calls and genotype likelihoods for sites in VCF" />
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234 </when>
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235 </conditional>
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236
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237
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238 <!-- reporting -->
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239 <conditional name="section_reporting_type">
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240 <param name="section_reporting_type_selector" type="select" label="Set Reporting options">
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241 <option value="do_not_set" selected="True">Do not set</option>
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242 <option value="set">Set</option>
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243 </param>
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244 <when value="do_not_set">
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245 <!-- do nothing here -->
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246 </when>
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247 <when value="set">
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248 <param name="pvar" type="float" label="Report sites if the probability that there is a polymorphism at the site is greater" value="0.0001" />
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249 <param name="show_reference_repeats" type="boolean" truevalue="--show-reference-repeats" falsevalue="" checked="False" label="Calculate and show information about reference repeats" />
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250 </when>
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251 </conditional>
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252
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253
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254 <!-- population model -->
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255 <conditional name="section_population_model_type">
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256 <param name="section_population_model_type_selector" type="select" label="Set population model options">
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257 <option value="do_not_set" selected="True">Do not set</option>
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258 <option value="set">Set</option>
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259 </param>
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260 <when value="do_not_set">
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261 <!-- do nothing here -->
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262 </when>
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263 <when value="set">
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264 <param name="theta" type="float" label="expected mutation rate or pairwise nucleotide diversity among the population" value="0.001" help="This serves as the single parameter to the Ewens Sampling Formula prior model"/>
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265 <param name="ploidy" type="integer" label="default ploidy for the analysis" value="2" />
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266 <param name="pooled" type="boolean" truevalue="--pooled" falsevalue="" checked="False" label="Assume that samples result from pooled sequencing" help="When using this flag, set --ploidy to the number of alleles in each sample." />
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267 </when>
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268 </conditional>
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269
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270 <!-- reference allele -->
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271 <conditional name="use_reference_allele_type">
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272 <param name="use_reference_allele_type_selector" type="select" label="Include the reference allele in the analysis">
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273 <option value="do_not_include_reference_allele" selected="True">Do not include</option>
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274 <option value="include_reference_allele">Include</option>
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275 </param>
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276 <when value="do_not_include_reference_allele">
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277 <!-- Do nothing here -->
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278 </when>
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279 <when value="include_reference_allele">
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280 <param name="diploid_reference" type="boolean" truevalue="--diploid-reference" falsevalue="" checked="False" label="Treat reference as diploid" />
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281 <param name="reference_quality_mq" type="integer" label="Assign mapping quality" value="100" />
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282 <param name="reference_quality_bq" type="integer" label="Assign base quality" value="60" />
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283 </when>
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284 </conditional>
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285
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286 <!-- allele scope -->
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287 <conditional name="section_allele_scope_type">
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288 <param name="section_allele_scope_type_selector" type="select" label="Set allele scope options">
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289 <option value="do_not_set" selected="True">Do not set</option>
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290 <option value="set">Set</option>
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291 </param>
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292 <when value="do_not_set">
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293 <!-- do nothing here -->
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294 </when>
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295 <when value="set">
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296 <param name="no_snps" type="boolean" truevalue="--no-snps" falsevalue="" checked="False" label="Ignore SNP alleles" />
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297 <param name="no_indels" type="boolean" truevalue="--no-indels" falsevalue="" checked="False" label="Ignore insertion and deletion alleles" />
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298 <param name="no_mnps" type="boolean" truevalue="--no-mnps" falsevalue="" checked="False" label="Ignore multi-nuceotide polymorphisms, MNPs" />
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299 <param name="no_complex" type="boolean" truevalue="--no-complex" falsevalue="" checked="False" label="Ignore complex events (composites of other classes)" />
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300 <param name="use_best_n_alleles" type="integer" label="Evaluate only the best N SNP alleles" value="0" min="0" help="Ranked by sum of supporting quality scores; Set to 0 to use all" />
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301 <param name="max_complex_gap" type="integer" label="Allow complex alleles with contiguous embedded matches of up to this length" value="" optional="True"/>
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302 </when>
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303 </conditional>
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304
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305 <!-- indel realignment -->
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306 <param name="left_align_indels" type="boolean" truevalue="--left-align-indels" falsevalue="" checked="False" label="Left-realign and merge gaps embedded in reads" />
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307
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308 <!-- input filters -->
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309 <conditional name="section_input_filters_type">
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310 <param name="section_input_filters_type_selector" type="select" label="Set input filters options">
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311 <option value="do_not_set" selected="True">Do not set</option>
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312 <option value="set">Set</option>
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313 </param>
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314 <when value="do_not_set">
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315 <!-- do nothing here -->
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316 </when>
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317 <when value="set">
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318 <param name="use_duplicate_reads" type="boolean" truevalue="--use-duplicate-reads" falsevalue="" checked="False" label="Include duplicate-marked alignments in the analysis" />
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319 <conditional name="no_filter_type">
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320 <param name="no_filter_type_selector" type="select" label="Apply filters">
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321 <option value="apply_filters" selected="True">Apply</option>
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322 <option value="no_filters">Do not apply</option>
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323 </param>
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324 <when value="no_filters">
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325 <!-- Do nothing here --> <!-- no-filters -->
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326 </when>
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327 <when value="apply_filters">
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328 <param name="min_mapping_quality" type="integer" label="Exclude alignments from analysis if they have a mapping quality less than" value="30" />
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329 <param name="min_base_quality" type="integer" label="Exclude alleles from analysis if their supporting base quality less than" value="20" />
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330 <param name="min_supporting_quality_mq" type="integer" label="In order to consider an alternate allele, at least one supporting alignment must have mapping quality" value="0" />
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331 <param name="min_supporting_quality_bq" type="integer" label="In order to consider an alternate allele, at least one supporting alignment must have base quality" value="0" />
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332 </when>
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333 </conditional>
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334 <param name="mismatch_base_quality_threshold" type="integer" label="Count mismatches toward read-mismatch-limit if the base quality of the mismatch is &gt;=" value="10" />
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335 <param name="read_mismatch_limit" type="integer" label="Exclude reads with more than N mismatches where each mismatch has base quality &gt;= mismatch-base-quality-threshold" value="" optional="True" />
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336 <param name="read_max_mismatch_fraction" type="float" label="Exclude reads with more than N [0,1] fraction of mismatches where each mismatch has base quality &gt;= mismatch-base-quality-threshold" value="1.0" />
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337 <param name="read_snp_limit" type="integer" label="Exclude reads with more than N base mismatches, ignoring gaps with quality &gt;= mismatch-base-quality-threshold" value="" optional="True" />
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338 <param name="read_indel_limit" type="integer" label="Exclude reads with more than N separate gaps" value="" optional="True" />
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339 <param name="indel_exclusion_window" type="integer" label="Ignore portions of alignments this many bases from a putative insertion or deletion allele" value="0" />
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340 <param name="min_alternate_fraction" type="float" label="Require at least this fraction of observations supporting an alternate allele within a single individual in the in order to evaluate the position" value="0" />
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341 <param name="min_alternate_count" type="integer" label="Require at least this count of observations supporting an alternate allele within a single individual in order to evaluate the position" value="1" />
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342 <param name="min_alternate_qsum" type="integer" label="Require at least this sum of quality of observations supporting an alternate allele within a single individual in order to evaluate the position" value="0" />
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343 <param name="min_alternate_total" type="integer" label="Require at least this count of observations supporting an alternate allele within the total population in order to use the allele in analysis" value="1" />
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344 <param name="min_coverage" type="integer" label="Require at least this coverage to process a site" value="0" />
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345 </when>
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346 </conditional>
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347
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348
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349 <!-- bayesian priors -->
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350 <conditional name="section_bayesian_priors_type">
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351 <param name="section_bayesian_priors_type_selector" type="select" label="Set bayesian priors options">
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352 <option value="do_not_set" selected="True">Do not set</option>
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353 <option value="set">Set</option>
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354 </param>
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355 <when value="do_not_set">
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356 <!-- do nothing here -->
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357 </when>
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358 <when value="set">
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359 <param name="no_ewens_priors" type="boolean" truevalue="--no-ewens-priors" falsevalue="" checked="False" label="Turns off the Ewens' Sampling Formula component of the priors" />
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360 <param name="no_population_priors" type="boolean" truevalue="--no-population-priors" falsevalue="" checked="False" label="No population priors" help="Equivalent to --pooled --no-ewens-priors" />
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361 <param name="hwe_priors" type="boolean" truevalue="--hwe-priors" falsevalue="" checked="False" label="Use the probability of the combination arising under HWE given the allele frequency as estimated by observation frequency" />
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362 </when>
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363 </conditional>
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364
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365 <!-- observation prior expectations -->
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366 <conditional name="section_observation_prior_expectations_type">
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367 <param name="section_observation_prior_expectations_type_selector" type="select" label="Set observation prior expectations options">
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368 <option value="do_not_set" selected="True">Do not set</option>
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369 <option value="set">Set</option>
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370 </param>
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371 <when value="do_not_set">
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372 <!-- do nothing here -->
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373 </when>
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374 <when value="set">
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375 <param name="binomial_obs_priors" type="boolean" truevalue="--binomial-obs-priors" falsevalue="" checked="False" label="Incorporate expectations about osbervations into the priors, Uses read placement probability, strand balance probability, and read position (5'-3') probability" />
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376 <param name="allele_balance_priors" type="boolean" truevalue="--allele-balance-priors" falsevalue="" checked="False" label="Use aggregate probability of observation balance between alleles as a component of the priors. Best for observations with minimal inherent reference bias" />
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377 </when>
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378 </conditional>
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379
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380
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381 <!-- algorithmic features -->
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382 <conditional name="section_algorithmic_features_type">
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383 <param name="section_algorithmic_features_type_selector" type="select" label="Set algorithmic features options">
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384 <option value="do_not_set" selected="True">Do not set</option>
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385 <option value="set">Set</option>
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386 </param>
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387 <when value="do_not_set">
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388 <!-- do nothing here -->
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389 </when>
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390 <when value="set">
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391 <param name="site_selection_max_iterations" type="integer" label="Uses hill-climbing algorithm to search posterior space for N iterations to determine if the site should be evaluated." value="5" help="Set to 0 to prevent use of this algorithm for site selection, and to a low integer for improvide site selection at a slight performance penalty" />
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392 <param name="genotyping_max_iterations" type="integer" label="Iterate no more than N times during genotyping step" value="25" />
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393 <param name="genotyping_max_banddepth" type="integer" label="Integrate no deeper than the Nth best genotype by likelihood when genotyping" value="6" />
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394 <param name="posterior_integration_limits_n" type="integer" label="Posteriror integration limit N" help="Integrate all genotype combinations in our posterior space which include no more than N samples with their Mth best data likelihood." value="1" />
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395 <param name="posterior_integration_limits_m" type="integer" label="Posteriror integration limit M" help="Integrate all genotype combinations in our posterior space which include no more than N samples with their Mth best data likelihood." value="3" />
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396 <param name="no_permute" type="boolean" truevalue="--no-permute" falsevalue="" checked="False" label="Do not scale prior probability of genotype combination given allele frequency by the number of permutations of included genotypes" />
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397 <param name="exclude_unobserved_genotypes" type="boolean" truevalue="--exclude-unobserved-genotypes" falsevalue="" checked="False" label="Skip sample genotypings for which the sample has no supporting reads" />
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398 <param name="genotype_variant_threshold" type="integer" label="Limit posterior integration to samples where the second-best genotype likelihood is no more than log(N) from the highest genotype likelihood for the sample" value="" optional="True" />
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399 <param name="use_mapping_quality" type="boolean" truevalue="--use-mapping-quality" falsevalue="" checked="False" label="Use mapping quality of alleles when calculating data likelihoods" />
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400 <param name="read_dependence_factor" type="float" label="Incorporate non-independence of reads by scaling successive observations by this factor during data likelihood calculations" value="0.9" />
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401 <param name="no_marginals" type="boolean" truevalue="--no-marginals" falsevalue="" checked="False" label="Do not calculate the marginal probability of genotypes. Saves time and improves scaling performance in large populations" />
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402 </when>
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403 </conditional>
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404
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405
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406 </when>
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407 </conditional>
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408
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409 </inputs>
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410 <outputs>
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411 <data format="vcf" name="output_vcf" label="${tool.name} on ${on_string} (variants)" />
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412 <data format="bed" name="output_failed_alleles_bed" label="${tool.name} on ${on_string} (failed alleles)">
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413 <filter>options_type['options_type_selector'] == "advanced" and options_type['output_failed_alleles_option'] is True</filter>
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414 </data>
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415 <data format="txt" name="output_trace" label="${tool.name} on ${on_string} (trace)">
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416 <filter>options_type['options_type_selector'] == "advanced" and options_type['output_trace_option'] is True</filter>
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417 </data>
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418 </outputs>
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419 <tests>
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420 <test>
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421 <param name="reference_source_selector" value="history" />
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422 <param name="ref_file" ftype="fasta" value="phiX.fasta"/>
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423 <param name="input_bam" ftype="bam" value="gatk/fake_phiX_reads_1.bam"/>
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424 <param name="options_type_selector" value="basic"/>
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425 <output name="output_vcf" file="variant_detection/freebayes/freebayes_out_1.vcf.contains" compare="contains"/>
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426 <!-- <output name="output_failed_alleles_bed" file="empty_file.dat" />
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427 <output name="output_trace" file="variant_detection/freebayes/freebayes_out_1.output_trace" /> -->
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428 </test>
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429 </tests>
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430 <help>
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431 **What it does**
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432
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433 This tool uses FreeBayes to call SNPS given a reference sequence and a BAM alignment file.
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434
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435 FreeBayes is a high-performance, flexible, and open-source Bayesian genetic variant detector. It operates on BAM alignment files, which are produced by most contemporary short-read aligners.
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436
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437 In addition to substantial performance improvements over its predecessors (PolyBayes, GigaBayes, and BamBayes), it expands the scope of SNP and small-indel variant calling to populations of individuals with heterogeneous copy number. FreeBayes is currently under active development.
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438
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439 Go `here &lt;http://bioinformatics.bc.edu/marthlab/FreeBayes&gt;`_ for details on FreeBayes.
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440
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441 ------
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442
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443 **Inputs**
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444
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445 FreeBayes accepts an input aligned BAM file.
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446
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447
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448 **Outputs**
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449
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450 The output is in the VCF format.
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451
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452 -------
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453
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454 **Settings**::
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455
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456 input and output:
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457
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458 -b --bam FILE Add FILE to the set of BAM files to be analyzed.
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459 -c --stdin Read BAM input on stdin.
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460 -v --vcf FILE Output VCF-format results to FILE.
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461 -f --fasta-reference FILE
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462 Use FILE as the reference sequence for analysis.
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463 An index file (FILE.fai) will be created if none exists.
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464 If neither --targets nor --region are specified, FreeBayes
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465 will analyze every position in this reference.
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466 -t --targets FILE
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467 Limit analysis to targets listed in the BED-format FILE.
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468 -r --region &lt;chrom&gt;:&lt;start_position&gt;..&lt;end_position&gt;
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469 Limit analysis to the specified region, 0-base coordinates,
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470 end_position not included (same as BED format).
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471 -s --samples FILE
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472 Limit analysis to samples listed (one per line) in the FILE.
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473 By default FreeBayes will analyze all samples in its input
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474 BAM files.
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475 --populations FILE
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476 Each line of FILE should list a sample and a population which
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477 it is part of. The population-based bayesian inference model
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478 will then be partitioned on the basis of the populations.
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479 -A --cnv-map FILE
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480 Read a copy number map from the BED file FILE, which has
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481 the format:
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482 reference sequence, start, end, sample name, copy number
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483 ... for each region in each sample which does not have the
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484 default copy number as set by --ploidy.
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485 -L --trace FILE Output an algorithmic trace to FILE.
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486 --failed-alleles FILE
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487 Write a BED file of the analyzed positions which do not
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488 pass --pvar to FILE.
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489 -@ --variant-input VCF
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490 Use variants reported in VCF file as input to the algorithm.
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491 A report will be generated for every record in the VCF file.
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492 -l --only-use-input-alleles
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493 Only provide variant calls and genotype likelihoods for sites
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494 and alleles which are provided in the VCF input, and provide
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495 output in the VCF for all input alleles, not just those which
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496 have support in the data.
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497
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498 reporting:
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499
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500 -P --pvar N Report sites if the probability that there is a polymorphism
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501 at the site is greater than N. default: 0.0001
61fe907fc37c Uploaded freebayes with tool dependencies
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parents:
diff changeset
502 -_ --show-reference-repeats
61fe907fc37c Uploaded freebayes with tool dependencies
devteam
parents:
diff changeset
503 Calculate and show information about reference repeats in
61fe907fc37c Uploaded freebayes with tool dependencies
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parents:
diff changeset
504 the VCF output.
61fe907fc37c Uploaded freebayes with tool dependencies
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parents:
diff changeset
505
61fe907fc37c Uploaded freebayes with tool dependencies
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parents:
diff changeset
506 population model:
61fe907fc37c Uploaded freebayes with tool dependencies
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parents:
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507
61fe907fc37c Uploaded freebayes with tool dependencies
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parents:
diff changeset
508 -T --theta N The expected mutation rate or pairwise nucleotide diversity
61fe907fc37c Uploaded freebayes with tool dependencies
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parents:
diff changeset
509 among the population under analysis. This serves as the
61fe907fc37c Uploaded freebayes with tool dependencies
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parents:
diff changeset
510 single parameter to the Ewens Sampling Formula prior model
61fe907fc37c Uploaded freebayes with tool dependencies
devteam
parents:
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511 default: 0.001
61fe907fc37c Uploaded freebayes with tool dependencies
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parents:
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512 -p --ploidy N Sets the default ploidy for the analysis to N. default: 2
61fe907fc37c Uploaded freebayes with tool dependencies
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diff changeset
513 -J --pooled Assume that samples result from pooled sequencing.
61fe907fc37c Uploaded freebayes with tool dependencies
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parents:
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514 When using this flag, set --ploidy to the number of
61fe907fc37c Uploaded freebayes with tool dependencies
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parents:
diff changeset
515 alleles in each sample.
61fe907fc37c Uploaded freebayes with tool dependencies
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parents:
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516
61fe907fc37c Uploaded freebayes with tool dependencies
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517 reference allele:
61fe907fc37c Uploaded freebayes with tool dependencies
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parents:
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518
61fe907fc37c Uploaded freebayes with tool dependencies
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parents:
diff changeset
519 -Z --use-reference-allele
61fe907fc37c Uploaded freebayes with tool dependencies
devteam
parents:
diff changeset
520 This flag includes the reference allele in the analysis as
61fe907fc37c Uploaded freebayes with tool dependencies
devteam
parents:
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521 if it is another sample from the same population.
61fe907fc37c Uploaded freebayes with tool dependencies
devteam
parents:
diff changeset
522 -H --diploid-reference
61fe907fc37c Uploaded freebayes with tool dependencies
devteam
parents:
diff changeset
523 If using the reference sequence as a sample (-Z),
61fe907fc37c Uploaded freebayes with tool dependencies
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parents:
diff changeset
524 treat it as diploid. default: false (reference is haploid)
61fe907fc37c Uploaded freebayes with tool dependencies
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parents:
diff changeset
525 --reference-quality MQ,BQ
61fe907fc37c Uploaded freebayes with tool dependencies
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parents:
diff changeset
526 Assign mapping quality of MQ to the reference allele at each
61fe907fc37c Uploaded freebayes with tool dependencies
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parents:
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527 site and base quality of BQ. default: 100,60
61fe907fc37c Uploaded freebayes with tool dependencies
devteam
parents:
diff changeset
528
61fe907fc37c Uploaded freebayes with tool dependencies
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parents:
diff changeset
529 allele scope:
61fe907fc37c Uploaded freebayes with tool dependencies
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parents:
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530
61fe907fc37c Uploaded freebayes with tool dependencies
devteam
parents:
diff changeset
531 -I --no-snps Ignore SNP alleles.
61fe907fc37c Uploaded freebayes with tool dependencies
devteam
parents:
diff changeset
532 -i --no-indels Ignore insertion and deletion alleles.
61fe907fc37c Uploaded freebayes with tool dependencies
devteam
parents:
diff changeset
533 -X --no-mnps Ignore multi-nuceotide polymorphisms, MNPs.
61fe907fc37c Uploaded freebayes with tool dependencies
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parents:
diff changeset
534 -u --no-complex Ignore complex events (composites of other classes).
61fe907fc37c Uploaded freebayes with tool dependencies
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parents:
diff changeset
535 -n --use-best-n-alleles N
61fe907fc37c Uploaded freebayes with tool dependencies
devteam
parents:
diff changeset
536 Evaluate only the best N SNP alleles, ranked by sum of
61fe907fc37c Uploaded freebayes with tool dependencies
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parents:
diff changeset
537 supporting quality scores. (Set to 0 to use all; default: all)
61fe907fc37c Uploaded freebayes with tool dependencies
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parents:
diff changeset
538 -E --max-complex-gap N
61fe907fc37c Uploaded freebayes with tool dependencies
devteam
parents:
diff changeset
539 Allow complex alleles with contiguous embedded matches of up
61fe907fc37c Uploaded freebayes with tool dependencies
devteam
parents:
diff changeset
540 to this length.
61fe907fc37c Uploaded freebayes with tool dependencies
devteam
parents:
diff changeset
541
61fe907fc37c Uploaded freebayes with tool dependencies
devteam
parents:
diff changeset
542 indel realignment:
61fe907fc37c Uploaded freebayes with tool dependencies
devteam
parents:
diff changeset
543
61fe907fc37c Uploaded freebayes with tool dependencies
devteam
parents:
diff changeset
544 -O --left-align-indels
61fe907fc37c Uploaded freebayes with tool dependencies
devteam
parents:
diff changeset
545 Left-realign and merge gaps embedded in reads. default: false
61fe907fc37c Uploaded freebayes with tool dependencies
devteam
parents:
diff changeset
546
61fe907fc37c Uploaded freebayes with tool dependencies
devteam
parents:
diff changeset
547 input filters:
61fe907fc37c Uploaded freebayes with tool dependencies
devteam
parents:
diff changeset
548
61fe907fc37c Uploaded freebayes with tool dependencies
devteam
parents:
diff changeset
549 -4 --use-duplicate-reads
61fe907fc37c Uploaded freebayes with tool dependencies
devteam
parents:
diff changeset
550 Include duplicate-marked alignments in the analysis.
61fe907fc37c Uploaded freebayes with tool dependencies
devteam
parents:
diff changeset
551 default: exclude duplicates
61fe907fc37c Uploaded freebayes with tool dependencies
devteam
parents:
diff changeset
552 -m --min-mapping-quality Q
61fe907fc37c Uploaded freebayes with tool dependencies
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parents:
diff changeset
553 Exclude alignments from analysis if they have a mapping
61fe907fc37c Uploaded freebayes with tool dependencies
devteam
parents:
diff changeset
554 quality less than Q. default: 30
61fe907fc37c Uploaded freebayes with tool dependencies
devteam
parents:
diff changeset
555 -q --min-base-quality Q
61fe907fc37c Uploaded freebayes with tool dependencies
devteam
parents:
diff changeset
556 Exclude alleles from analysis if their supporting base
61fe907fc37c Uploaded freebayes with tool dependencies
devteam
parents:
diff changeset
557 quality is less than Q. default: 20
61fe907fc37c Uploaded freebayes with tool dependencies
devteam
parents:
diff changeset
558 -R --min-supporting-quality MQ,BQ
61fe907fc37c Uploaded freebayes with tool dependencies
devteam
parents:
diff changeset
559 In order to consider an alternate allele, at least one supporting
61fe907fc37c Uploaded freebayes with tool dependencies
devteam
parents:
diff changeset
560 alignment must have mapping quality MQ, and one supporting
61fe907fc37c Uploaded freebayes with tool dependencies
devteam
parents:
diff changeset
561 allele must have base quality BQ. default: 0,0, unset
61fe907fc37c Uploaded freebayes with tool dependencies
devteam
parents:
diff changeset
562 -Q --mismatch-base-quality-threshold Q
61fe907fc37c Uploaded freebayes with tool dependencies
devteam
parents:
diff changeset
563 Count mismatches toward --read-mismatch-limit if the base
61fe907fc37c Uploaded freebayes with tool dependencies
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parents:
diff changeset
564 quality of the mismatch is &gt;= Q. default: 10
61fe907fc37c Uploaded freebayes with tool dependencies
devteam
parents:
diff changeset
565 -U --read-mismatch-limit N
61fe907fc37c Uploaded freebayes with tool dependencies
devteam
parents:
diff changeset
566 Exclude reads with more than N mismatches where each mismatch
61fe907fc37c Uploaded freebayes with tool dependencies
devteam
parents:
diff changeset
567 has base quality &gt;= mismatch-base-quality-threshold.
61fe907fc37c Uploaded freebayes with tool dependencies
devteam
parents:
diff changeset
568 default: ~unbounded
61fe907fc37c Uploaded freebayes with tool dependencies
devteam
parents:
diff changeset
569 -z --read-max-mismatch-fraction N
61fe907fc37c Uploaded freebayes with tool dependencies
devteam
parents:
diff changeset
570 Exclude reads with more than N [0,1] fraction of mismatches where
61fe907fc37c Uploaded freebayes with tool dependencies
devteam
parents:
diff changeset
571 each mismatch has base quality &gt;= mismatch-base-quality-threshold
61fe907fc37c Uploaded freebayes with tool dependencies
devteam
parents:
diff changeset
572 default: 1.0
61fe907fc37c Uploaded freebayes with tool dependencies
devteam
parents:
diff changeset
573 -$ --read-snp-limit N
61fe907fc37c Uploaded freebayes with tool dependencies
devteam
parents:
diff changeset
574 Exclude reads with more than N base mismatches, ignoring gaps
61fe907fc37c Uploaded freebayes with tool dependencies
devteam
parents:
diff changeset
575 with quality &gt;= mismatch-base-quality-threshold.
61fe907fc37c Uploaded freebayes with tool dependencies
devteam
parents:
diff changeset
576 default: ~unbounded
61fe907fc37c Uploaded freebayes with tool dependencies
devteam
parents:
diff changeset
577 -e --read-indel-limit N
61fe907fc37c Uploaded freebayes with tool dependencies
devteam
parents:
diff changeset
578 Exclude reads with more than N separate gaps.
61fe907fc37c Uploaded freebayes with tool dependencies
devteam
parents:
diff changeset
579 default: ~unbounded
61fe907fc37c Uploaded freebayes with tool dependencies
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diff changeset
580 -0 --no-filters Do not use any input base and mapping quality filters
61fe907fc37c Uploaded freebayes with tool dependencies
devteam
parents:
diff changeset
581 Equivalent to -m 0 -q 0 -R 0 -S 0
61fe907fc37c Uploaded freebayes with tool dependencies
devteam
parents:
diff changeset
582 -x --indel-exclusion-window
61fe907fc37c Uploaded freebayes with tool dependencies
devteam
parents:
diff changeset
583 Ignore portions of alignments this many bases from a
61fe907fc37c Uploaded freebayes with tool dependencies
devteam
parents:
diff changeset
584 putative insertion or deletion allele. default: 0
61fe907fc37c Uploaded freebayes with tool dependencies
devteam
parents:
diff changeset
585 -F --min-alternate-fraction N
61fe907fc37c Uploaded freebayes with tool dependencies
devteam
parents:
diff changeset
586 Require at least this fraction of observations supporting
61fe907fc37c Uploaded freebayes with tool dependencies
devteam
parents:
diff changeset
587 an alternate allele within a single individual in the
61fe907fc37c Uploaded freebayes with tool dependencies
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parents:
diff changeset
588 in order to evaluate the position. default: 0.0
61fe907fc37c Uploaded freebayes with tool dependencies
devteam
parents:
diff changeset
589 -C --min-alternate-count N
61fe907fc37c Uploaded freebayes with tool dependencies
devteam
parents:
diff changeset
590 Require at least this count of observations supporting
61fe907fc37c Uploaded freebayes with tool dependencies
devteam
parents:
diff changeset
591 an alternate allele within a single individual in order
61fe907fc37c Uploaded freebayes with tool dependencies
devteam
parents:
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592 to evaluate the position. default: 1
61fe907fc37c Uploaded freebayes with tool dependencies
devteam
parents:
diff changeset
593 -3 --min-alternate-qsum N
61fe907fc37c Uploaded freebayes with tool dependencies
devteam
parents:
diff changeset
594 Require at least this sum of quality of observations supporting
61fe907fc37c Uploaded freebayes with tool dependencies
devteam
parents:
diff changeset
595 an alternate allele within a single individual in order
61fe907fc37c Uploaded freebayes with tool dependencies
devteam
parents:
diff changeset
596 to evaluate the position. default: 0
61fe907fc37c Uploaded freebayes with tool dependencies
devteam
parents:
diff changeset
597 -G --min-alternate-total N
61fe907fc37c Uploaded freebayes with tool dependencies
devteam
parents:
diff changeset
598 Require at least this count of observations supporting
61fe907fc37c Uploaded freebayes with tool dependencies
devteam
parents:
diff changeset
599 an alternate allele within the total population in order
61fe907fc37c Uploaded freebayes with tool dependencies
devteam
parents:
diff changeset
600 to use the allele in analysis. default: 1
61fe907fc37c Uploaded freebayes with tool dependencies
devteam
parents:
diff changeset
601 -! --min-coverage N
61fe907fc37c Uploaded freebayes with tool dependencies
devteam
parents:
diff changeset
602 Require at least this coverage to process a site. default: 0
61fe907fc37c Uploaded freebayes with tool dependencies
devteam
parents:
diff changeset
603
61fe907fc37c Uploaded freebayes with tool dependencies
devteam
parents:
diff changeset
604 bayesian priors:
61fe907fc37c Uploaded freebayes with tool dependencies
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parents:
diff changeset
605
61fe907fc37c Uploaded freebayes with tool dependencies
devteam
parents:
diff changeset
606 -Y --no-ewens-priors
61fe907fc37c Uploaded freebayes with tool dependencies
devteam
parents:
diff changeset
607 Turns off the Ewens' Sampling Formula component of the priors.
61fe907fc37c Uploaded freebayes with tool dependencies
devteam
parents:
diff changeset
608 -k --no-population-priors
61fe907fc37c Uploaded freebayes with tool dependencies
devteam
parents:
diff changeset
609 Equivalent to --pooled --no-ewens-priors
61fe907fc37c Uploaded freebayes with tool dependencies
devteam
parents:
diff changeset
610 -w --hwe-priors Use the probability of the combination arising under HWE given
61fe907fc37c Uploaded freebayes with tool dependencies
devteam
parents:
diff changeset
611 the allele frequency as estimated by observation frequency.
61fe907fc37c Uploaded freebayes with tool dependencies
devteam
parents:
diff changeset
612
61fe907fc37c Uploaded freebayes with tool dependencies
devteam
parents:
diff changeset
613 observation prior expectations:
61fe907fc37c Uploaded freebayes with tool dependencies
devteam
parents:
diff changeset
614
61fe907fc37c Uploaded freebayes with tool dependencies
devteam
parents:
diff changeset
615 -V --binomial-obs-priors
61fe907fc37c Uploaded freebayes with tool dependencies
devteam
parents:
diff changeset
616 Incorporate expectations about osbervations into the priors,
61fe907fc37c Uploaded freebayes with tool dependencies
devteam
parents:
diff changeset
617 Uses read placement probability, strand balance probability,
61fe907fc37c Uploaded freebayes with tool dependencies
devteam
parents:
diff changeset
618 and read position (5'-3') probability.
61fe907fc37c Uploaded freebayes with tool dependencies
devteam
parents:
diff changeset
619 -a --allele-balance-priors
61fe907fc37c Uploaded freebayes with tool dependencies
devteam
parents:
diff changeset
620 Use aggregate probability of observation balance between alleles
61fe907fc37c Uploaded freebayes with tool dependencies
devteam
parents:
diff changeset
621 as a component of the priors. Best for observations with minimal
61fe907fc37c Uploaded freebayes with tool dependencies
devteam
parents:
diff changeset
622 inherent reference bias.
61fe907fc37c Uploaded freebayes with tool dependencies
devteam
parents:
diff changeset
623
61fe907fc37c Uploaded freebayes with tool dependencies
devteam
parents:
diff changeset
624 algorithmic features:
61fe907fc37c Uploaded freebayes with tool dependencies
devteam
parents:
diff changeset
625
61fe907fc37c Uploaded freebayes with tool dependencies
devteam
parents:
diff changeset
626 -M --site-selection-max-iterations N
61fe907fc37c Uploaded freebayes with tool dependencies
devteam
parents:
diff changeset
627 Uses hill-climbing algorithm to search posterior space for N
61fe907fc37c Uploaded freebayes with tool dependencies
devteam
parents:
diff changeset
628 iterations to determine if the site should be evaluated. Set to 0
61fe907fc37c Uploaded freebayes with tool dependencies
devteam
parents:
diff changeset
629 to prevent use of this algorithm for site selection, and
61fe907fc37c Uploaded freebayes with tool dependencies
devteam
parents:
diff changeset
630 to a low integer for improvide site selection at a slight
61fe907fc37c Uploaded freebayes with tool dependencies
devteam
parents:
diff changeset
631 performance penalty. default: 5.
61fe907fc37c Uploaded freebayes with tool dependencies
devteam
parents:
diff changeset
632 -B --genotyping-max-iterations N
61fe907fc37c Uploaded freebayes with tool dependencies
devteam
parents:
diff changeset
633 Iterate no more than N times during genotyping step. default: 25.
61fe907fc37c Uploaded freebayes with tool dependencies
devteam
parents:
diff changeset
634 --genotyping-max-banddepth N
61fe907fc37c Uploaded freebayes with tool dependencies
devteam
parents:
diff changeset
635 Integrate no deeper than the Nth best genotype by likelihood when
61fe907fc37c Uploaded freebayes with tool dependencies
devteam
parents:
diff changeset
636 genotyping. default: 6.
61fe907fc37c Uploaded freebayes with tool dependencies
devteam
parents:
diff changeset
637 -W --posterior-integration-limits N,M
61fe907fc37c Uploaded freebayes with tool dependencies
devteam
parents:
diff changeset
638 Integrate all genotype combinations in our posterior space
61fe907fc37c Uploaded freebayes with tool dependencies
devteam
parents:
diff changeset
639 which include no more than N samples with their Mth best
61fe907fc37c Uploaded freebayes with tool dependencies
devteam
parents:
diff changeset
640 data likelihood. default: 1,3.
61fe907fc37c Uploaded freebayes with tool dependencies
devteam
parents:
diff changeset
641 -K --no-permute
61fe907fc37c Uploaded freebayes with tool dependencies
devteam
parents:
diff changeset
642 Do not scale prior probability of genotype combination given allele
61fe907fc37c Uploaded freebayes with tool dependencies
devteam
parents:
diff changeset
643 frequency by the number of permutations of included genotypes.
61fe907fc37c Uploaded freebayes with tool dependencies
devteam
parents:
diff changeset
644 -N --exclude-unobserved-genotypes
61fe907fc37c Uploaded freebayes with tool dependencies
devteam
parents:
diff changeset
645 Skip sample genotypings for which the sample has no supporting reads.
61fe907fc37c Uploaded freebayes with tool dependencies
devteam
parents:
diff changeset
646 -S --genotype-variant-threshold N
61fe907fc37c Uploaded freebayes with tool dependencies
devteam
parents:
diff changeset
647 Limit posterior integration to samples where the second-best
61fe907fc37c Uploaded freebayes with tool dependencies
devteam
parents:
diff changeset
648 genotype likelihood is no more than log(N) from the highest
61fe907fc37c Uploaded freebayes with tool dependencies
devteam
parents:
diff changeset
649 genotype likelihood for the sample. default: ~unbounded
61fe907fc37c Uploaded freebayes with tool dependencies
devteam
parents:
diff changeset
650 -j --use-mapping-quality
61fe907fc37c Uploaded freebayes with tool dependencies
devteam
parents:
diff changeset
651 Use mapping quality of alleles when calculating data likelihoods.
61fe907fc37c Uploaded freebayes with tool dependencies
devteam
parents:
diff changeset
652 -D --read-dependence-factor N
61fe907fc37c Uploaded freebayes with tool dependencies
devteam
parents:
diff changeset
653 Incorporate non-independence of reads by scaling successive
61fe907fc37c Uploaded freebayes with tool dependencies
devteam
parents:
diff changeset
654 observations by this factor during data likelihood
61fe907fc37c Uploaded freebayes with tool dependencies
devteam
parents:
diff changeset
655 calculations. default: 0.9
61fe907fc37c Uploaded freebayes with tool dependencies
devteam
parents:
diff changeset
656 -= --no-marginals
61fe907fc37c Uploaded freebayes with tool dependencies
devteam
parents:
diff changeset
657 Do not calculate the marginal probability of genotypes. Saves
61fe907fc37c Uploaded freebayes with tool dependencies
devteam
parents:
diff changeset
658 time and improves scaling performance in large populations.
61fe907fc37c Uploaded freebayes with tool dependencies
devteam
parents:
diff changeset
659
61fe907fc37c Uploaded freebayes with tool dependencies
devteam
parents:
diff changeset
660
61fe907fc37c Uploaded freebayes with tool dependencies
devteam
parents:
diff changeset
661 ------
61fe907fc37c Uploaded freebayes with tool dependencies
devteam
parents:
diff changeset
662
61fe907fc37c Uploaded freebayes with tool dependencies
devteam
parents:
diff changeset
663 **Citation**
61fe907fc37c Uploaded freebayes with tool dependencies
devteam
parents:
diff changeset
664
61fe907fc37c Uploaded freebayes with tool dependencies
devteam
parents:
diff changeset
665 For the underlying tool, please cite `FreeBayes &lt;http://bioinformatics.bc.edu/marthlab/FreeBayes&gt;`_.
61fe907fc37c Uploaded freebayes with tool dependencies
devteam
parents:
diff changeset
666
61fe907fc37c Uploaded freebayes with tool dependencies
devteam
parents:
diff changeset
667 If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.*
61fe907fc37c Uploaded freebayes with tool dependencies
devteam
parents:
diff changeset
668
61fe907fc37c Uploaded freebayes with tool dependencies
devteam
parents:
diff changeset
669 </help>
61fe907fc37c Uploaded freebayes with tool dependencies
devteam
parents:
diff changeset
670 </tool>