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annotate freebayes.xml @ 25:bf27106652f3 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
author iuc
date Wed, 08 Feb 2017 12:45:05 -0500
parents da6e10dee68b
children a028d13cd860
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bf27106652f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
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1 <tool id="freebayes" name="FreeBayes" version="@DEPENDENCY_VERSION@-2">
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2 <description>bayesian genetic variant detector</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <requirements>
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7 <requirement type="package" version="@DEPENDENCY_VERSION@">freebayes</requirement>
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8 <requirement type="package" version="0.1.19">samtools</requirement>
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9 <requirement type="package" version="4.1.3">gawk</requirement>
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10 <requirement type="package" version="20160622">parallel</requirement>
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11 </requirements>
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12 <stdio>
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13 <exit_code range="1:" />
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14 </stdio>
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15 <command><![CDATA[
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16 ##set up input files
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17
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18 #set $reference_fasta_filename = "localref.fa"
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19
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20 #if str( $reference_source.reference_source_selector ) == "history":
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21 ln -s -f '${reference_source.ref_file}' '${reference_fasta_filename}' &&
bf27106652f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
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22 samtools faidx '${reference_fasta_filename}' 2>&1 || echo "Error running samtools faidx for FreeBayes" >&2 &&
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23 #else:
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24 #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path )
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25 #end if
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27 #for $bam_count, $input_bam in enumerate( $reference_source.input_bams ):
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28 ln -s -f '${input_bam}' 'b_${bam_count}.bam' &&
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29 ln -s -f '${input_bam.metadata.bam_index}' 'b_${bam_count}.bam.bai' &&
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30 #end for
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32 ## Tabixize optional input_variant_vcf file (for --variant-input option)
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33 #if ( str( $options_type.options_type_selector ) == 'cline' or str( $options_type.options_type_selector ) == 'full' ) and str( $options_type.optional_inputs.optional_inputs_selector ) == 'set' and str( $options_type.optional_inputs.input_variant_type.input_variant_type_selector ) == "provide_vcf":
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34 ln -s -f '${options_type.optional_inputs.input_variant_type.input_variant_vcf}' 'input_variant_vcf.vcf.gz' &&
bf27106652f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
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35 ln -s -f '${Tabixized_input}' 'input_variant_vcf.vcf.gz.tbi' &&
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36 #end if
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37
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38 #for $bam_count, $input_bam in enumerate( $reference_source.input_bams ):
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39 samtools view -H b_${bam_count}.bam |
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40 grep "^@SQ" |
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41 cut -f 2- |
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42 awk '{ gsub("^SN:","",$1);
bf27106652f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
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43 gsub("^LN:","",$2);
bf27106652f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
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44 print $1"\t0\t"$2; }' >> regions_all.bed &&
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45 #end for
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47 sort -u regions_all.bed > regions_uniq.bed &&
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48 ## split into even small chunks, this has some disatvantages and will not be used for the moment
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49 ## bedtools makewindows -b regions_uniq.bed -w 10000000 -s 9990000 > regions.bed &&
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51 mkdir vcf_output &&
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52 mkdir failed_alleles &&
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53 mkdir trace &&
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55 ## Finished setting up inputs
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57 for i in `cat regions_uniq.bed | awk '{print $1":"$2".."$3}'`;
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58 do
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60 echo "
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62 ## COMMAND LINE STARTS HERE
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63
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64 freebayes
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65
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66 --region '\$i'
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67
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68 #for $bam_count, $input_bam in enumerate( $reference_source.input_bams ):
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69 --bam 'b_${bam_count}.bam'
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70 #end for
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71 --fasta-reference '${reference_fasta_filename}'
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72
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73 ## Outputs
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74 --vcf './vcf_output/part_\$i.vcf'
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75
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76 #if str( $target_limit_type.target_limit_type_selector ) == "limit_by_target_file":
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77 --targets '${target_limit_type.input_target_bed}'
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78 #elif str( $target_limit_type.target_limit_type_selector ) == "limit_by_region":
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79 --region '${target_limit_type.region_chromosome}:${target_limit_type.region_start}..${target_limit_type.region_end}'
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80 #end if
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81
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82 ##advanced options
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83 #if str( $options_type.options_type_selector ) == "simple":
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84 ##do nothing as command like build up to this point is sufficinet for simple diploid calling
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85
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86 #elif str( $options_type.options_type_selector ) == "simple_w_filters":
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87 --standard-filters
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88 --min-coverage '${options_type.min_coverage}'
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89 #elif str( $options_type.options_type_selector ) == "naive":
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90 --haplotype-length 0
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91 --min-alternate-count 1
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92 --min-alternate-fraction 0
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93 --pooled-continuous
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94 --report-monomorphic
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95 #elif str( $options_type.options_type_selector ) == "naive_w_filters":
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96 --haplotype-length 0
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97 --min-alternate-count 1
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98 --min-alternate-fraction 0
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99 --pooled-continuous
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100 --report-monomorphic
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101 --standard-filters
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102 --min-coverage '${options_type.min_coverage}'
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103
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104 ## Command line direct text entry is not allowed at this time for security reasons
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105 #elif str( $options_type.options_type_selector ) == "full":
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106 #if str( $options_type.optional_inputs.optional_inputs_selector ) == 'set':
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107 ${options_type.optional_inputs.report_monomorphic}
23
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108
25
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109 #if $options_type.optional_inputs.output_trace_option:
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110 --trace ./trace/part_'\$i'.txt
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111 #end if
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112 #if $options_type.optional_inputs.output_failed_alleles_option:
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113 --failed-alleles ./failed_alleles/part_'\$i'.bed
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114 #end if
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115 #if $options_type.optional_inputs.samples:
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116 --samples '${options_type.optional_inputs.samples}'
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117 #end if
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118 #if $options_type.optional_inputs.populations:
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119 --populations '${options_type.optional_inputs.populations}'
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120 #end if
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121 #if $options_type.optional_inputs.A:
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122 --cnv-map '${options_type.optional_inputs.A}'
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123 #end if
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124 #if str( $options_type.optional_inputs.input_variant_type.input_variant_type_selector ) == "provide_vcf":
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125 --variant-input 'input_variant_vcf.vcf.gz' ## input_variant_vcf.vcf.gz is symlinked to a galaxy-generated dataset in "Tabixize optional input_variant_vcf file" section of the command line above
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126 ${options_type.optional_inputs.input_variant_type.only_use_input_alleles}
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127 #end if
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128 #if $options_type.optional_inputs.haplotype_basis_alleles:
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129 --haplotype-basis-alleles '${options_type.optional_inputs.haplotype_basis_alleles}'
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130 #end if
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131 #if $options_type.optional_inputs.observation_bias:
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132 --observation-bias '${options_type.optional_inputs.observation_bias}'
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133 #end if
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134 #if $options_type.optional_inputs.contamination_estimates:
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135 --contamination-estimates '${options_type.optional_inputs.contamination_estimates}'
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136 #end if
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137 #end if
23
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138
25
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139 ## REPORTING
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140 #if str( $options_type.reporting.reporting_selector ) == "set":
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141 --pvar ${options_type.reporting.pvar}
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142 #end if
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143 ## POPULATION MODEL
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144 #if str( $options_type.population_model.population_model_selector ) == "set":
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145 --theta '${options_type.population_model.T}'
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146 --ploidy '${options_type.population_model.P}'
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147 ${options_type.population_model.J}
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148 ${options_type.population_model.K}
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149 #end if
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150
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151 ## REFERENCE ALLELE
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152 #if str( $options_type.reference_allele.reference_allele_selector ) == "set":
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153 ${options_type.reference_allele.Z}
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154 --reference-quality '${options_type.reference_allele.reference_quality}'
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155 #end if
13
2dd40b601766 Uploaded
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156
25
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157 ## ALLELE SCOPE
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158 #if str( $options_type.allele_scope.allele_scope_selector ) == "set":
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159 ${options_type.allele_scope.I}
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160 ${options_type.allele_scope.i}
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161 ${options_type.allele_scope.X}
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162 ${options_type.allele_scope.u}
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163 ${options_type.allele_scope.no_partial_observations}
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164
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165 -n '${options_type.allele_scope.n}'
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166
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167 --haplotype-length '${options_type.allele_scope.haplotype_length}'
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168 --min-repeat-size '${options_type.allele_scope.min_repeat_length}'
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169 --min-repeat-entropy '${options_type.allele_scope.min_repeat_entropy}'
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170 #end if
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171
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172 ## REALIGNMENT
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173 ${options_type.O}
23
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174
25
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175 ##INPUT FILTERS
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176 #if str( $options_type.input_filters.input_filters_selector ) == "set":
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177 ${options_type.input_filters.use_duplicate_reads}
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178 -m '${options_type.input_filters.m}'
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179 -q '${options_type.input_filters.q}'
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180 -R '${options_type.input_filters.R}'
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181 -Y '${options_type.input_filters.Y}'
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182 -e '${options_type.input_filters.e}'
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183 -F '${options_type.input_filters.F}'
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184 -C '${options_type.input_filters.C}'
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185 -G '${options_type.input_filters.G}'
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186
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187 #if str( $options_type.input_filters.mismatch_filters.mismatch_filters_selector ) == "set":
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188 -Q '${options_type.input_filters.mismatch_filters.Q}'
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189 -U '${options_type.input_filters.mismatch_filters.U}'
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190 -z '${options_type.input_filters.mismatch_filters.z}'
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191
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192 --read-snp-limit '${options_type.input_filters.mismatch_filters.read_snp_limit}'
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193 #end if
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194
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195 --min-coverage '${options_type.input_filters.min_coverage}'
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196 --min-alternate-qsum "${options_type.input_filters.min_alternate_qsum}"
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197 #end if
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198
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199 ## POPULATION AND MAPPABILITY PRIORS
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200 #if str( $options_type.population_mappability_priors.population_mappability_priors_selector ) == "set":
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201 ${options_type.population_mappability_priors.k}
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202 ${options_type.population_mappability_priors.w}
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203 ${options_type.population_mappability_priors.V}
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204 ${options_type.population_mappability_priors.a}
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205 #end if
25
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206
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207 ## GENOTYPE LIKELIHOODS
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208 #if str( $options_type.genotype_likelihoods.genotype_likelihoods_selector ) == "set":
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209 ${$options_type.genotype_likelihoods.experimental_gls}
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210
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211 --base-quality-cap '${$options_type.genotype_likelihoods.base_quality_cap}'
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212 --prob-contamination '${$options_type.genotype_likelihoods.prob_contamination}'
23
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213 #end if
25
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214
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215 ## ALGORITHMIC FEATURES
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216 #if str( $options_type.algorithmic_features.algorithmic_features_selector ) == "set":
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217 -B '${options_type.algorithmic_features.B}'
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218 -W '${options_type.algorithmic_features.W}'
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219 -D '${options_type.algorithmic_features.D}'
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220
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221 #if str( $options_type.algorithmic_features.genotype_variant_threshold.genotype_variant_threshold_selector ) == "set":
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222 -S '${options_type.algorithmic_features.genotype_variant_threshold.S}'
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223 #end if
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224
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225 ${options_type.algorithmic_features.N}
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226 ${options_type.algorithmic_features.j}
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227 ${options_type.algorithmic_features.H}
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228 ${options_type.algorithmic_features.genotype_qualities}
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229 ${options_type.algorithmic_features.report_genotype_likelihood_max}
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230
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231 --genotyping-max-banddepth '${options_type.algorithmic_features.genotyping_max_banddepth}'
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232 #end if
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233 #end if
20
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234
25
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235 ";
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236 done > freebayes_commands.sh &&
23
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237
25
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238 cat freebayes_commands.sh |
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239 parallel --no-notice -j \${GALAXY_SLOTS:-1} &&
23
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240
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241 ## make VCF header
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242 grep "^#" "./vcf_output/part_\$i.vcf" > header.txt &&
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243
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244 for i in `cat regions_uniq.bed | awk '{print $1":"$2".."$3}'`;
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245 do
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246 ## if this fails then it bails out the script
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247 cat "./vcf_output/part_\$i.vcf" | grep -v "^#" || true
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248 ;
25
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249 done | sort -k1,1 -k2,2n -k5,5 -u | cat header.txt - > '${output_vcf}'
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250
23
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251 #if str( $options_type.options_type_selector ) == "full":
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252 #if str( $options_type.optional_inputs.optional_inputs_selector ) == 'set':
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253 #if $options_type.optional_inputs.output_failed_alleles_option:
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254 &&
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255 for i in `cat regions.bed | awk '{print $1":"$2".."$3}'`;
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256 do
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257 cat "./failed_alleles/part_\$i.bed"
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258 ;
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259 done > '${output_failed_alleles_bed}'
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260 #end if
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261
23
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262 #if $options_type.optional_inputs.output_trace_option:
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263 &&
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264 for i in `cat regions.bed | awk '{print $1":"$2".."$3}'`;
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265 do
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266 cat './trace/part_\$i.txt'
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267 ;
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268 done > '${output_trace}'
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269 #end if
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270 #end if
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271 #end if
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272 ]]></command>
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273
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274 <inputs>
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275 <conditional name="reference_source">
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276 <param name="reference_source_selector" type="select" label="Choose the source for the reference genome">
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277 <option value="cached">Locally cached</option>
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278 <option value="history">History</option>
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279 </param>
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280 <when value="cached">
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281 <param name="input_bams" type="data" format="bam" multiple="True" label="BAM file">
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282 <validator type="unspecified_build" />
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283 <validator type="dataset_metadata_in_data_table" table_name="fasta_indexes" metadata_name="dbkey" metadata_column="1" message="Sequences are not currently available for the specified build." />
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284 </param>
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285 <param name="ref_file" type="select" label="Using reference genome">
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286 <options from_data_table="fasta_indexes"></options>
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287 <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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288 </param>
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289 </when>
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290 <when value="history"> <!-- FIX ME!!!! -->
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291 <param name="input_bams" type="data" format="bam" multiple="True" label="BAM file" />
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292 <param name="ref_file" type="data" format="fasta" label="Use the following dataset as the reference sequence"
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293 help="You can upload a FASTA sequence to the history and use it as reference" />
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294 </when>
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295 </conditional>
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296 <conditional name="target_limit_type">
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297 <param name="target_limit_type_selector" type="select" label="Limit variant calling to a set of regions?" help="Sets --targets or --region options">
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298 <option value="do_not_limit" selected="True">Do not limit</option>
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299 <option value="limit_by_target_file">Limit by target file</option>
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300 <option value="limit_by_region">Limit to region</option>
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301 </param>
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302 <when value="do_not_limit" /><!-- Do nothing here -->
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303 <when value="limit_by_target_file">
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304 <param name="input_target_bed" type="data" format="bed" label="Limit analysis to regions in a file (BED-format)." argument="--targets"/>
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305 </when>
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306 <when value="limit_by_region">
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307 <param name="region_chromosome" type="text" label="Region Chromosome" value="" argument="--region"/> <!--only once? -->
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308 <param name="region_start" type="integer" label="Region Start" value="" />
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309 <param name="region_end" type="integer" label="Region End" value="" />
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310 </when>
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311 </conditional>
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312 <conditional name="options_type">
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313 <param name="options_type_selector" type="select" label="Choose parameter selection level"
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314 help="Select how much control over the freebayes run you need" >
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315 <option value="simple" selected="True">1. Simple diploid calling</option>
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316 <option value="simple_w_filters">2. Simple diploid calling with filtering and coverage</option>
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317 <option value="naive">3. Frequency-based pooled calling</option>
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318 <option value="naive_w_filters">4. Frequency-based pooled calling with filtering and coverage</option>
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319 <option value="full">5. Full list of options</option>
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320 </param>
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321 <when value="full">
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322 <conditional name="optional_inputs">
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323 <param name="optional_inputs_selector" type="select" label="Additional inputs"
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324 help="Sets --samples, --populations, --cnv-map, --trace, --failed-alleles, --varinat-input, --only-use-input-alleles, --haplotype-basis-alleles,
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325 --report-all-haplotype-alleles, --report-monomorphic options, --observation-bias, and --contamination-estimates">
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326 <option value="do_not_set" selected="true">Do not provide additional inputs</option>
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327 <option value="set">Provide additional inputs</option>
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328 </param>
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329 <when value="set">
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330 <param name="output_failed_alleles_option" type="boolean" truevalue="--failed-alleles" falsevalue="" checked="False"
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331 label="Write out failed alleles file" argument="--failed-alleles" />
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332 <param name="output_trace_option" type="boolean" truevalue="--trace" falsevalue="" checked="False"
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333 label="Write out algorithm trace file" argument="--trace"/>
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334 <param name="samples" type="data" format="txt" label="Limit analysis to samples listed (one per line) in the FILE" optional="True"
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335 help="default=By default FreeBayes will analyze all samples in its input BAM files" argument="--samples"/>
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336 <param name="populations" type="data" format="txt" label="Populations File" optional="True"
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337 help="Each line of FILE should list a sample and a population which it is part of. The population-based bayesian inference model will
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338 then be partitioned on the basis of the populations. [default=False]"
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339 argument="--populations" />
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340 <param name="A" type="data" format="bed" label="Read a copy number map from the BED file FILE" optional="True"
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341 help="default=copy number is set to as specified by --ploidy. Read a copy number map from the BED file FILE, which has the format:
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342 reference sequence, start, end, sample name, copy number ... for each region in each sample which does not have the default copy number as set by --ploidy."
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343 argument="--cnv-map" />
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344 <conditional name="input_variant_type">
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345 <param name="input_variant_type_selector" type="select" label="Provide variants file">
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346 <option value="do_not_provide" selected="True">Do not provide</option>
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347 <option value="provide_vcf">Provide VCF file</option>
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348 </param>
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349 <when value="do_not_provide" /><!-- Do nothing here -->
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350 <when value="provide_vcf">
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351 <param name="input_variant_vcf" type="data" format="vcf_bgzip" label="Use variants reported in VCF file as input to the algorithm" argument="--variant-input">
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352 <conversion name="Tabixized_input" type="tabix" />
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353 </param>
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354 <param name="only_use_input_alleles" type="boolean" truevalue="--only-use-input-alleles" falsevalue="" checked="False"
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355 label="Only provide variant calls and genotype likelihoods for sites in VCF" argument="--only-use-input-alleles" />
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356 </when>
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357 </conditional>
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358 <param name="haplotype_basis_alleles" type="data" format="vcf" label="Only use variant alleles provided in this input VCF for the construction of complex or haplotype alleles" optional="True"
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359 argument="--haplotype-basis-alleles" />
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360 <param name="report_monomorphic" type="boolean" truevalue="--report-monomorphic" falsevalue="" checked="False"
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diff changeset
361 label="Report even loci which appear to be monomorphic, and report all considered alleles, even those which are not in called genotypes."
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362 argument="--report-monomorphic" />
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363 <param name="observation_bias" optional="True" type="data" format="tabular" label="Load read length-dependent allele observation biases from"
25
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364 help="The format is [length] [alignment efficiency relative to reference] where the efficiency is 1 if there is no relative observation bias"
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365 argument="--observation-bias" />
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366 <param name="contamination_estimates" optional="True" type="data" format="tabular" label="Upload per-sample estimates of contamination from"
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367 help="The format should be: sample p(read=R|genotype=AR) p(read=A|genotype=AA) Sample '*' can be used to set default contamination estimates."
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368 argument="--contamination-estimates" />
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369 </when>
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370 <when value="do_not_set" /><!-- do nothing -->
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371 </conditional>
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372
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diff changeset
373 <!-- reporting -->
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374 <conditional name="reporting">
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375 <param name="reporting_selector" type="select" label="Reporting options" help="Sets -P --pvar option">
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376 <option value="do_not_set" selected="True">Use defaults</option>
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377 <option value="set">Set reporting options</option>
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378 </param>
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379 <when value="set">
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380 <param name="pvar" type="float" value="0.0" label="Report sites if the probability that there is a polymorphism at the site is greater than"
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381 help="Note that post-filtering is generally recommended over the use of this parameter. [default=0.0]"
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382 argument="--pvar" />
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383 </when>
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384 <when value="do_not_set" /><!-- do nothing -->
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385 </conditional>
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386
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387 <!-- population model -->
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388 <conditional name="population_model">
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389 <param name="population_model_selector" type="select" label="Population model options"
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390 help="Sets --theta, --ploidy, --pooled-discrete, and --pooled-continuous options " >
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391 <option value="do_not_set" selected="true">Use defaults</option>
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392 <option value="set">Set population model options</option>
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393 </param>
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diff changeset
394 <when value="set">
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395 <param name="T" type="float" value="0.001" label="The expected mutation rate or pairwise nucleotide diversity among the population under analysis"
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396 help="This serves as the single parameter to the Ewens Sampling Formula prior model. [default = 0.001]" argument='--theta'/>
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397 <param name="P" type="integer" value="2" label="Set ploidy for the analysis"
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398 help="default=2" argument='--ploidy' />
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399 <param name="J" type="boolean" truevalue="-J" falsevalue="" checked="False" label="Assume that samples result from pooled sequencing"
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400 help="Model pooled samples using discrete genotypes across pools. When using this flag, set --ploidy to the number of alleles in each sample or use the --cnv-map to define per-sample ploidy. [default=False]"
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401 argument="--pooled-discrete"/>
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402 <param name="K" type="boolean" truevalue="-K" falsevalue="" checked="False" label="Output all alleles which pass input filters, regardles of genotyping outcome or model"
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403 help="default=False." argument="--poled-continuous" />
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404 </when>
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405 <when value="do_not_set" /><!-- do nothing -->
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406 </conditional>
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407
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408 <!-- reference allele -->
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409 <conditional name="reference_allele">
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410 <param name="reference_allele_selector" type="select" label="Reference allele options"
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411 help="Sets --use-reference-allele and --reference-quality options.">
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412 <option value="do_not_set" selected="true">Use defaults</option>
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413 <option value="set">Set reference allele options</option>
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414 </param>
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diff changeset
415 <when value="set">
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416 <param name="Z" type="boolean" truevalue="-Z" falsevalue="" checked="False" label="Include the reference allele in the analysis as if it is another sample from the same population"
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417 help="default=False" argument="--use-reference-allele" />
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418 <param name="reference_quality" type="text" value="100,60" label="Assign mapping quality of MQ (100) to the reference allele at each site and base quality of BQ (60)"
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419 help="default=100,60" argument="--reference-quality" />
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420 </when>
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421 <when value="do_not_set" /><!-- do nothing -->
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422 </conditional>
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423
23
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diff changeset
424 <!-- allelic scope -->
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425 <conditional name="allele_scope">
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426 <param name="allele_scope_selector" type="select" label="Allelic scope options"
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427 help="Sets -I, i, -X, -u, -n, --haplotype-length, --min-repeat-size, --min-repeat-entropy, and --no-partial-observations options.">
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428 <option value="do_not_set" selected="true">Use defaults</option>
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429 <option value="set">Set alleic scope options</option>
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430 </param>
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431 <when value="set">
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432 <param name="I" type="boolean" truevalue="-I" falsevalue="" checked="False" label="Ignore SNP alleles"
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433 help="default=False" argument="--no-snps" />
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parents: 24
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434 <param name="i" type="boolean" truevalue="-i" falsevalue="" checked="False" label="Ignore indels alleles"
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diff changeset
435 help="default=False" argument="--no-indels" />
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parents: 24
diff changeset
436 <param name="X" type="boolean" truevalue="-X" falsevalue="" checked="False" label="Ignore multi-nucleotide polymorphisms, MNPs"
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parents: 24
diff changeset
437 help="default=False" argument="--no-mnps" />
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diff changeset
438 <param name="u" type="boolean" truevalue="-u" falsevalue="" checked="False" label="Ignore complex events (composites of other classes)."
25
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diff changeset
439 help="default=False" argument="--no-complex" />
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diff changeset
440 <param name="n" type="integer" value="0" label="How many best SNP alleles to evaluate"
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parents: 24
diff changeset
441 help="Alleles are ranked by the sum of supporting quality scores. Set to 0 to evaluate all. [default=0 (all)]"
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diff changeset
442 argument="--use-best-n-alleles" />
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diff changeset
443 <param name="haplotype_length" type="integer" value="3" label="Allow haplotype calls with contiguous embedded matches of up to (nucleotides)"
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parents: 24
diff changeset
444 help="-E --max-complex-gap --haplotype-length; default=3." />
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parents: 22
diff changeset
445 <param name="min_repeat_length" type="integer" value="5" label="When assembling observations across repeats, require the total repeat length at least this many bp"
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parents: 24
diff changeset
446 help="default=5." argument="--min-repeat-size" />
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parents: 22
diff changeset
447 <param name="min_repeat_entropy" type="integer" value="0" label="To detect interrupted repeats, build across sequence until it has entropy > (bits per bp)"
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parents: 24
diff changeset
448 help="default=0 (off)." argument="--min-repeat-entropy" />
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parents: 22
diff changeset
449 <param name="no_partial_observations" type="boolean" truevalue="--no-partial-observations" falsevalue="" checked="False"
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parents: 24
diff changeset
450 label="Exclude observations which do not fully span the dynamically-determined detection window"
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parents: 24
diff changeset
451 help="default=use all observations, dividing partial support across matching haplotypes when generating haplotypes."
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parents: 24
diff changeset
452 argument="--no-partial-observations" />
23
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diff changeset
453 </when>
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parents: 24
diff changeset
454 <when value="do_not_set" /><!-- do nothing -->
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diff changeset
455 </conditional>
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parents: 24
diff changeset
456
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diff changeset
457 <!-- indel realignment -->
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parents: 24
diff changeset
458 <param name="O" type="boolean" truevalue="-O" falsevalue="" checked="False" label="Turn off left-alignment of indels"
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parents: 24
diff changeset
459 help="default=False (do left align)." argument="--dont-left-align-indels" />
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parents: 24
diff changeset
460
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parents: 22
diff changeset
461 <!-- input filters -->
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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parents: 22
diff changeset
462 <conditional name="input_filters">
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diff changeset
463 <param name="input_filters_selector" type="select" label="Input filters"
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parents: 24
diff changeset
464 help="Sets -4, -m, -q, -R, -Y, -Q, -U, -z, -&#36;, -e, -0, -F, -C, -3, -G, and -&#33; options.">
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diff changeset
465 <option value="do_not_set" selected="true">No input filters (default)</option>
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diff changeset
466 <option value="set">Set input filters</option>
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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parents: 22
diff changeset
467 </param>
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parents: 24
diff changeset
468 <when value="set">
23
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parents: 22
diff changeset
469 <param name="use_duplicate_reads" type="boolean" truevalue="--use-duplicate-reads" falsevalue="" checked="False"
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parents: 24
diff changeset
470 label="Include duplicate-marked alignments in the analysis."
bf27106652f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
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parents: 24
diff changeset
471 help="default=False (exclude duplicates marked as such in alignments)." argument="--use-duplicate-reads" />
23
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parents: 22
diff changeset
472 <param name="m" type="integer" value="1" label="Exclude alignments from analysis if they have a mapping quality less than"
25
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parents: 24
diff changeset
473 help="default=1" argument="--min-mapping-quality" />
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parents: 22
diff changeset
474 <param name="q" type="integer" value="0" label="Exclude alleles from analysis if their supporting base quality less than"
25
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parents: 24
diff changeset
475 help="default=0" argument="--min-base-quality" />
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parents: 22
diff changeset
476 <param name="R" type="integer" value="0" label="Consider any allele in which the sum of qualities of supporting observations is at least"
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parents: 24
diff changeset
477 help="default=0" argument="--min-supporting-allele-qsum" />
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parents: 22
diff changeset
478 <param name="Y" type="integer" value="0" label="Consider any allele in which and the sum of mapping qualities of supporting reads is at least"
25
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parents: 24
diff changeset
479 help="default=0" argument="--min-supporting-mapping-qsum" />
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parents: 22
diff changeset
480 <conditional name="mismatch_filters">
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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parents: 22
diff changeset
481 <param name="mismatch_filters_selector" type="select" label="Mismatch filters"
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parents: 24
diff changeset
482 help="Sets -Q, -U, -z, and &#36; options">
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parents: 22
diff changeset
483 <option value="do_not_set" selected="true">No mismatch filters (default)</option>
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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parents: 22
diff changeset
484 <option value="set">Set mismatch filters</option>
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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parents: 22
diff changeset
485 </param>
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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parents: 22
diff changeset
486 <when value="set">
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parents: 24
diff changeset
487 <param name="Q" type="integer" value="10"
bf27106652f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
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parents: 24
diff changeset
488 label="Count mismatches toward -U (option below) if the base quality of the mismatch is >="
bf27106652f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
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parents: 24
diff changeset
489 help="default=10" argument="--mismatch-base-quality-threshold" />
bf27106652f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
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parents: 24
diff changeset
490 <param name="U" type="integer" value="1000" optional="True"
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parents: 24
diff changeset
491 label="Exclude reads with more than N mismatches where each mismatch has base quality >= Q (option above)"
bf27106652f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
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parents: 24
diff changeset
492 help="default=~unbound" argument="--read-mismatch-limit" />
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parents: 22
diff changeset
493 <param name="z" type="float" value="1.0" min="0.0" max="1.0"
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parents: 24
diff changeset
494 label="Exclude reads with more than N [0,1] fraction of mismatches where each mismatch has base quality >= Q (second option above)"
bf27106652f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
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parents: 24
diff changeset
495 help="default=1.0" argument="--read-max-mismatch-fraction" />
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parents: 22
diff changeset
496 <param name="read_snp_limit" type="integer"
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parents: 24
diff changeset
497 value="1000" label="Exclude reads with more than N base mismatches, ignoring gaps with quality >= Q (third option abobe)"
bf27106652f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
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parents: 24
diff changeset
498 argument="--read-snp-limit" />
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diff changeset
499 </when>
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parents: 24
diff changeset
500 <when value="do_not_set" /><!-- do nothing -->
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parents: 22
diff changeset
501 </conditional>
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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parents: 22
diff changeset
502 <param name="e" type="integer" value="1000" label="Exclude reads with more than this number of separate gaps"
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parents: 24
diff changeset
503 help="default=~unbounded" argument="--read-snp-limit" />
bf27106652f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
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parents: 24
diff changeset
504 <param name="standard_filters" type="boolean" truevalue="-0" falsevalue="" checked="False"
bf27106652f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
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parents: 24
diff changeset
505 label="Use stringent input base and mapping quality filters"
bf27106652f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
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parents: 24
diff changeset
506 help="default=False. Equivalent to -m 30 -q 20 -R 0 -S 0" argument="--standard-filters"/>
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parents: 22
diff changeset
507 <param name="F" type="float" value="0.2"
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parents: 24
diff changeset
508 label="Require at least this fraction of observations supporting an alternate allele within a single individual in the in order to evaluate the position"
bf27106652f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
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parents: 24
diff changeset
509 help="default=0.2" argument="--min-alternate-fraction" />
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parents: 22
diff changeset
510 <param name="C" type="integer" value="2"
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parents: 24
diff changeset
511 label="Require at least this count of observations supporting an alternate allele within a single individual in order to evaluate the position"
bf27106652f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
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parents: 24
diff changeset
512 help="default=2" argument="--min-alternate-count" />
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parents: 22
diff changeset
513 <param name="min_alternate_qsum" type="integer" value="0"
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parents: 24
diff changeset
514 label="Require at least this sum of quality of observations supporting an alternate allele within a single individual in order to evaluate the position"
bf27106652f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
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parents: 24
diff changeset
515 help="default=0" argument="--min-alternate-qsum" />
23
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diff changeset
516 <param name="G" type="integer" value="1"
25
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iuc
parents: 24
diff changeset
517 label="Require at least this count of observations supporting an alternate allele within the total population in order to use the allele in analysis"
bf27106652f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 24
diff changeset
518 help="default=1" argument="--min-alternate-total" />
bf27106652f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 24
diff changeset
519 <expand macro="par_min_cov" />
23
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parents: 22
diff changeset
520 </when>
25
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iuc
parents: 24
diff changeset
521 <when value="do_not_set" /><!-- do nothing -->
23
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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parents: 22
diff changeset
522 </conditional>
25
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parents: 24
diff changeset
523
23
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parents: 22
diff changeset
524 <!-- population and mappability priors -->
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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parents: 22
diff changeset
525 <conditional name="population_mappability_priors">
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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parents: 22
diff changeset
526 <param name="population_mappability_priors_selector" type="select" label="Population and mappability priors"
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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parents: 22
diff changeset
527 help="Sets -k, -w, -V, and -a options.">
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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parents: 22
diff changeset
528 <option value="do_not_set" selected="true">Use defaults</option>
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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parents: 22
diff changeset
529 <option value="set">Set population and mappability priors</option>
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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parents: 22
diff changeset
530 </param>
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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parents: 22
diff changeset
531 <when value="set">
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parents: 22
diff changeset
532 <param name="k" type="boolean" truevalue="-k" falsevalue="" checked="False" label="No population priors"
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parents: 24
diff changeset
533 help="default=False. Equivalent to --pooled-discrete --hwe-priors-off and removal of Ewens Sampling Formula component of priors."
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parents: 24
diff changeset
534 argument="--no-population-priors" />
23
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parents: 22
diff changeset
535 <param name="w" type="boolean" truevalue="-w" falsevalue="" checked="False"
25
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parents: 24
diff changeset
536 label="Disable estimation of the probability of the combination arising under HWE given the allele frequency as estimated by observation frequency"
bf27106652f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
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parents: 24
diff changeset
537 help="default=False" argument="--hwe-priors-off" />
23
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parents: 22
diff changeset
538 <param name="V" type="boolean" truevalue="-V" falsevalue="" checked="False" label="Disable incorporation of prior expectations about observations"
25
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parents: 24
diff changeset
539 help="default=False. Uses read placement probability, strand balance probability, and read position (5&#39;'-3&#39;') probability."
bf27106652f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
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parents: 24
diff changeset
540 argument="--binomial-obs-priors-off" />
23
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parents: 22
diff changeset
541 <param name="a" type="boolean" truevalue="-a" falsevalue="" checked="False"
25
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iuc
parents: 24
diff changeset
542 label="Disable use of aggregate probability of observation balance between alleles as a component of the priors"
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iuc
parents: 24
diff changeset
543 help="default=False"
bf27106652f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 24
diff changeset
544 argument="--allele-balance-priors-off" />
23
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parents: 22
diff changeset
545 </when>
25
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iuc
parents: 24
diff changeset
546 <when value="do_not_set" /><!-- do nothing -->
23
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parents: 22
diff changeset
547 </conditional>
25
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iuc
parents: 24
diff changeset
548
23
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parents: 22
diff changeset
549 <!-- genotype likelihoods -->
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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parents: 22
diff changeset
550 <conditional name="genotype_likelihoods">
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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parents: 22
diff changeset
551 <param name="genotype_likelihoods_selector" type="select" label="Genotype likelihood options"
25
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parents: 24
diff changeset
552 help="Sets --base-quality-cap, --experimental-gls, and --prob-contamination options.">
23
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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parents: 22
diff changeset
553 <option value="do_not_set" selected="true">Use defaults</option>
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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parents: 22
diff changeset
554 <option value="set">Set genotype likelihood options</option>
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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parents: 22
diff changeset
555 </param>
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 22
diff changeset
556 <when value="set">
25
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iuc
parents: 24
diff changeset
557 <param name="base_quality_cap" type="integer" value="0" label="Limit estimated observation quality by capping base quality at"
bf27106652f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 24
diff changeset
558 argument="--base-quality-cap" />
23
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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parents: 22
diff changeset
559 <param name="experimental_gls" type="boolean" truevalue="--experimental-gls" falsevalue="" checked="False"
25
bf27106652f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 24
diff changeset
560 label="Generate genotype likelihoods using 'effective base depth' metric qual = 1-BaseQual * 1-MapQual"
bf27106652f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 24
diff changeset
561 help="Incorporate partial observations. This is the default when contamination estimates are provided. Optimized for diploid samples."
bf27106652f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 24
diff changeset
562 argument="--experimental-gls" />
23
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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parents: 22
diff changeset
563 <param name="prob_contamination" type="float" value="10e-9" label="An estimate of contamination to use for all samples"
25
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iuc
parents: 24
diff changeset
564 help="default=10e-9." argument="--prob-contamination" />
23
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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parents: 22
diff changeset
565 </when>
25
bf27106652f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 24
diff changeset
566 <when value="do_not_set" /><!-- do nothing -->
23
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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parents: 22
diff changeset
567 </conditional>
25
bf27106652f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 24
diff changeset
568
23
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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parents: 22
diff changeset
569 <!-- algorithmic features -->
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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parents: 22
diff changeset
570 <conditional name="algorithmic_features">
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 22
diff changeset
571 <param name="algorithmic_features_selector" type="select" label="Algorithmic features"
25
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iuc
parents: 24
diff changeset
572 help="Sets --report-genotypes-likelihood-max, -B, --genotyping-max-banddepth, -W, -N, S, -j, -H, -D, -= options">
23
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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parents: 22
diff changeset
573 <option value="do_not_set" selected="true">Use defaults</option>
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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parents: 22
diff changeset
574 <option value="set">Set algorithmic features</option>
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 22
diff changeset
575 </param>
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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parents: 22
diff changeset
576 <when value="set">
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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parents: 22
diff changeset
577 <param name="report_genotype_likelihood_max" type="boolean" truevalue="--report-genotype-likelihood-max" falsevalue="" checked="False"
25
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iuc
parents: 24
diff changeset
578 label="Report genotypes using the maximum-likelihood estimate provided from genotype likelihoods."
bf27106652f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 24
diff changeset
579 help="default=False" argument="--report-genotype-likelihood-max" />
23
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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parents: 22
diff changeset
580 <param name="B" type="integer" value="1000" label="Iterate no more than N times during genotyping step"
25
bf27106652f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
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parents: 24
diff changeset
581 help="default=1000." argument="--genotyping-max-iterations" />
23
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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parents: 22
diff changeset
582 <param name="genotyping_max_banddepth" type="integer" value="6" label="Integrate no deeper than the Nth best genotype by likelihood when genotyping"
25
bf27106652f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 24
diff changeset
583 help="default=6" argument="--genotyping-max-banddepth" />
23
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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parents: 22
diff changeset
584 <param name="W" type="text" value="1,3"
25
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iuc
parents: 24
diff changeset
585 label="Integrate all genotype combinations in our posterior space which include no more than N (1) samples with their Mth (3) best data likelihood"
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iuc
parents: 24
diff changeset
586 help="default=1,3" argument="--posterior-integration-limits" />
23
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devteam
parents: 22
diff changeset
587 <param name="N" type="boolean" truevalue="--exclude-unobserved-genotypes" falsevalue="" checked="False"
25
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iuc
parents: 24
diff changeset
588 label="Skip sample genotypings for which the sample has no supporting reads"
bf27106652f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 24
diff changeset
589 help="default=False" argument="--exclude-unobserved-genotypes" />
23
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parents: 22
diff changeset
590 <conditional name="genotype_variant_threshold">
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 22
diff changeset
591 <param name="genotype_variant_threshold_selector" type="select"
25
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iuc
parents: 24
diff changeset
592 label="Limit posterior integration" argument="--genotype-variant-threshold">
23
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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parents: 22
diff changeset
593 <option value="do_not_set" selected="true">Do not limit posterior integration</option>
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 22
diff changeset
594 <option value="set">Set posterior integration limit</option>
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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parents: 22
diff changeset
595 </param>
25
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iuc
parents: 24
diff changeset
596 <when value="do_not_set" /><!-- do nothing -->
23
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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parents: 22
diff changeset
597 <when value="set">
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598 <param name="S" value="" type="integer"
25
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599 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."
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600 help="default=~unbounded" argument="--genotype-variant-threshold" />
23
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601 </when>
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602 </conditional>
25
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603 <param name="j" type="boolean" truevalue="-j" falsevalue="" checked="False"
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604 label="Use mapping quality of alleles when calculating data likelihoods"
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605 help="default=False" argument="--use-mapping-quality" />
23
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606 <param name="H" type="boolean" truevalue="-H" falsevalue="" checked="False"
25
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607 label="Use a weighted sum of base qualities around an indel, scaled by the distance from the indel"
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608 help="default=use a minimum Base Quality in flanking sequence." argument="--harmonic-indel-quality" />
23
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609 <param name="D" type="float" value="0.9" label="Incorporate non-independence of reads by scaling successive observations by this factor during data likelihood calculations"
25
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610 help="default=0.9." argument="--read-dependence-factor" />
23
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611 <param name="genotype_qualities" type="boolean" truevalue="--genotype-qualities" falsevalue="" checked="False"
25
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612 label="Calculate the marginal probability of genotypes and report as GQ in each sample field in the VCF output"
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613 help="-= --genotype-qualities; default=False " />
23
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614 </when>
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615 <when value="do_not_set" /><!-- do nothing -->
23
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616 </conditional>
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617 </when>
25
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618 <when value="simple" /><!-- do nothing -->
23
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619 <when value="simple_w_filters">
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620 <!-- add standard-filters to command line -->
25
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621 <expand macro="par_min_cov" />
23
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622 </when>
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623 <when value="naive">
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624 <!-- do nothing build command line using haplotype-length 0 min-alternate-count 1 min-alternate-fraction 0 pooled-continuous report-monomorphic -->
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625 </when>
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626 <when value="naive_w_filters">
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627 <!-- do nothing build command line using haplotype-length 0 min-alternate-count 1 min-alternate-fraction 0 pooled-continuous report-monomorphic standard-filters-->
25
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628 <expand macro="par_min_cov" />
23
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629 </when>
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630 </conditional>
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631 </inputs>
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632 <outputs>
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633 <data format="vcf" name="output_vcf" label="${tool.name} on ${on_string} (variants)" />
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634 <data format="bed" name="output_failed_alleles_bed" label="${tool.name} on ${on_string} (failed alleles)">
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635 <filter>( options_type['options_type_selector'] == 'cline' or options_type['options_type_selector'] == 'full' ) and options_type['optional_inputs']['optional_inputs_selector'] == 'set' and options_type['optional_inputs']['output_failed_alleles_option'] is True</filter>
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636 </data>
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637 <data format="txt" name="output_trace" label="${tool.name} on ${on_string} (trace)">
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638 <filter>( options_type['options_type_selector'] == 'cline' or options_type['options_type_selector'] == 'full' ) and options_type['optional_inputs']['optional_inputs_selector'] == 'set' and options_type['optional_inputs']['output_trace_option'] is True</filter>
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639 </data>
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640 </outputs>
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641 <tests>
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642 <test>
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643 <param name="reference_source_selector" value="history" />
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644 <param name="ref_file" ftype="fasta" value="freebayes-phix174.fasta"/>
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645 <param name="input_bams" ftype="bam" value="freebayes-phix174.bam"/>
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646 <param name="options_type_selector" value="simple"/>
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647 <output name="output_vcf" file="freebayes-phix174-test1.vcf" compare="contains"/>
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648 </test>
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649 <test>
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650 <param name="reference_source_selector" value="history" />
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651 <param name="ref_file" ftype="fasta" value="freebayes-phix174.fasta"/>
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652 <param name="input_bams" ftype="bam" value="freebayes-phix174.bam"/>
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653 <param name="options_type_selector" value="naive_w_filters"/>
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654 <param name="min_coverage" value="14"/>
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655 <output name="output_vcf" file="freebayes-phix174-test2.vcf" compare="contains"/>
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656 </test>
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657 <test>
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658 <param name="reference_source_selector" value="history" />
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659 <param name="ref_file" ftype="fasta" value="freebayes-phix174.fasta"/>
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660 <param name="input_bams" ftype="bam" value="freebayes-phix174.bam"/>
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661 <param name="options_type_selector" value="naive_w_filters"/>
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662 <param name="min_coverage" value="14"/>
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663 <output name="output_vcf" file="freebayes-phix174-test3.vcf" compare="contains"/>
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664 </test>
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665 <test>
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666 <param name="reference_source_selector" value="history" />
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667 <param name="ref_file" ftype="fasta" value="freebayes-phix174.fasta"/>
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668 <param name="input_bams" ftype="bam" value="freebayes-phix174.bam"/>
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669 <param name="options_type_selector" value="full"/>
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670 <param name="population_model_selector" value="set"/>
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671 <param name="P" value="1"/>
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672 <output name="output_vcf" file="freebayes-phix174-test4.vcf" compare="contains"/>
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673 </test>
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674 </tests>
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675 <help>
13
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676 **What it does**
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677
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678 FreeBayes is a Bayesian genetic variant detector designed to find small polymorphisms, specifically SNPs (single-nucleotide polymorphisms), indels (insertions and deletions), MNPs (multi-nucleotide polymorphisms), and complex events (composite insertion and substitution events) smaller than the length of a short-read sequencing alignment.
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679
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680 See https://github.com/ekg/freebayes for details on FreeBayes.
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681
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682 ------
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683
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684 **Description**
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685
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686 Privided BAM file(s) and a reference. FreeBayes will provide VCF output on standard out describing SNPs, indels, and complex variants in samples in the input alignments.
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687
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parents:
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688 By default, FreeBayes will consider variants supported by at least 2 observations in a single sample (-C) and also by at least 20% of the reads from a single sample (-F). These settings are suitable to low to high depth sequencing in haploid and diploid samples, but users working with polyploid or pooled samples may wish to adjust them depending on the characteristics of their sequencing data.
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devteam
parents:
diff changeset
689
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devteam
parents:
diff changeset
690 FreeBayes is capable of calling variant haplotypes shorter than a read length where multiple polymorphisms segregate on the same read. The maximum distance between polymorphisms phased in this way is determined by the --max-complex-gap, which defaults to 3bp. In practice, this can comfortably be set to half the read length.
2dd40b601766 Uploaded
devteam
parents:
diff changeset
691
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devteam
parents:
diff changeset
692 Ploidy may be set to any level (-p), but by default all samples are assumed to be diploid. FreeBayes can model per-sample and per-region variation in copy-number (-A) using a copy-number variation map.
2dd40b601766 Uploaded
devteam
parents:
diff changeset
693
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devteam
parents:
diff changeset
694 FreeBayes can act as a frequency-based pooled caller and describe variants and haplotypes in terms of observation frequency rather than called genotypes. To do so, use --pooled-continuous and set input filters to a suitable level. Allele observation counts will be described by AO and RO fields in the VCF output.
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devteam
parents:
diff changeset
695
2dd40b601766 Uploaded
devteam
parents:
diff changeset
696 -------
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devteam
parents:
diff changeset
697
2dd40b601766 Uploaded
devteam
parents:
diff changeset
698 **Galaxy-specific options**
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devteam
parents:
diff changeset
699
25
bf27106652f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 24
diff changeset
700 Galaxy allows five levels of control over FreeBayes options provided by **Choose parameter selection level** menu option. These are:
13
2dd40b601766 Uploaded
devteam
parents:
diff changeset
701
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devteam
parents:
diff changeset
702 1. *Simple diploid calling*: The simples possible FreeBayes application. Equvalent of using FreeBayes with only a BAM input and no other parameter options.
25
bf27106652f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 24
diff changeset
703 2. *Simple diploid calling with filtering and coverage*: Same as #1 plus two additional options: -0 (standard filters: --min-mapping-quality 30 --min-base-quality 20 --min-supporting-allele-qsum 0 --genotype-varinat-threshold 0) and --min-coverage.
bf27106652f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 24
diff changeset
704 3. *Frequency-based pooled calling*: This is equivalent to using FreeBayes with the following options: --haplotype-length 0 --min-alternate-count 1 --min-alternate-fraction 0 --pooled-continuous --report-monomorphic. This is the best choice for calling varinats in mixtures such as viral, bacterial, or organellar genomes.
13
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devteam
parents:
diff changeset
705 4. *Frequency-based pooled calling with filtering and coverage*: Same as #3 but adds -0 and --min-coverage like in #2.
2dd40b601766 Uploaded
devteam
parents:
diff changeset
706 5. *Complete list of all options*: Gives you full control by exposing all FreeBayes options as Galaxy widgets.
2dd40b601766 Uploaded
devteam
parents:
diff changeset
707
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devteam
parents:
diff changeset
708 -----
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devteam
parents:
diff changeset
709
2dd40b601766 Uploaded
devteam
parents:
diff changeset
710 **FreeBayes options**
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devteam
parents:
diff changeset
711
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devteam
parents:
diff changeset
712 .. class:: infomark
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devteam
parents:
diff changeset
713
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devteam
parents:
diff changeset
714 Note that each Galaxy parameter widget corresponding to command line flags listed below:
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devteam
parents:
diff changeset
715
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devteam
parents:
diff changeset
716 Input and output::
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devteam
parents:
diff changeset
717
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devteam
parents:
diff changeset
718 -t --targets FILE
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devteam
parents:
diff changeset
719 Limit analysis to targets listed in the BED-format FILE.
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devteam
parents:
diff changeset
720 -r --region chrom:start_position-end_position
2dd40b601766 Uploaded
devteam
parents:
diff changeset
721 Limit analysis to the specified region, 0-base coordinates,
2dd40b601766 Uploaded
devteam
parents:
diff changeset
722 end_position included. Either '-' or '..' maybe used as a separator.
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devteam
parents:
diff changeset
723 -s --samples FILE
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devteam
parents:
diff changeset
724 Limit analysis to samples listed (one per line) in the FILE.
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devteam
parents:
diff changeset
725 By default FreeBayes will analyze all samples in its input
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devteam
parents:
diff changeset
726 BAM files.
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devteam
parents:
diff changeset
727 --populations FILE
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devteam
parents:
diff changeset
728 Each line of FILE should list a sample and a population which
2dd40b601766 Uploaded
devteam
parents:
diff changeset
729 it is part of. The population-based bayesian inference model
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devteam
parents:
diff changeset
730 will then be partitioned on the basis of the populations.
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devteam
parents:
diff changeset
731 -A --cnv-map FILE
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devteam
parents:
diff changeset
732 Read a copy number map from the BED file FILE, which has
2dd40b601766 Uploaded
devteam
parents:
diff changeset
733 the format:
2dd40b601766 Uploaded
devteam
parents:
diff changeset
734 reference sequence, start, end, sample name, copy number
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devteam
parents:
diff changeset
735 ... for each region in each sample which does not have the
2dd40b601766 Uploaded
devteam
parents:
diff changeset
736 default copy number as set by --ploidy.
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devteam
parents:
diff changeset
737 --trace FILE Output an algorithmic trace to FILE.
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devteam
parents:
diff changeset
738 --failed-alleles FILE
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devteam
parents:
diff changeset
739 Write a BED file of the analyzed positions which do not
2dd40b601766 Uploaded
devteam
parents:
diff changeset
740 pass --pvar to FILE.
2dd40b601766 Uploaded
devteam
parents:
diff changeset
741 -@ --variant-input VCF
2dd40b601766 Uploaded
devteam
parents:
diff changeset
742 Use variants reported in VCF file as input to the algorithm.
2dd40b601766 Uploaded
devteam
parents:
diff changeset
743 Variants in this file will be treated as putative variants
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devteam
parents:
diff changeset
744 even if there is not enough support in the data to pass
2dd40b601766 Uploaded
devteam
parents:
diff changeset
745 input filters.
2dd40b601766 Uploaded
devteam
parents:
diff changeset
746 -l --only-use-input-alleles
2dd40b601766 Uploaded
devteam
parents:
diff changeset
747 Only provide variant calls and genotype likelihoods for sites
2dd40b601766 Uploaded
devteam
parents:
diff changeset
748 and alleles which are provided in the VCF input, and provide
2dd40b601766 Uploaded
devteam
parents:
diff changeset
749 output in the VCF for all input alleles, not just those which
2dd40b601766 Uploaded
devteam
parents:
diff changeset
750 have support in the data.
2dd40b601766 Uploaded
devteam
parents:
diff changeset
751 --haplotype-basis-alleles VCF
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devteam
parents:
diff changeset
752 When specified, only variant alleles provided in this input
2dd40b601766 Uploaded
devteam
parents:
diff changeset
753 VCF will be used for the construction of complex or haplotype
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devteam
parents:
diff changeset
754 alleles.
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devteam
parents:
diff changeset
755 --report-all-haplotype-alleles
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devteam
parents:
diff changeset
756 At sites where genotypes are made over haplotype alleles,
2dd40b601766 Uploaded
devteam
parents:
diff changeset
757 provide information about all alleles in output, not only
2dd40b601766 Uploaded
devteam
parents:
diff changeset
758 those which are called.
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devteam
parents:
diff changeset
759 --report-monomorphic
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devteam
parents:
diff changeset
760 Report even loci which appear to be monomorphic, and report all
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devteam
parents:
diff changeset
761 considered alleles, even those which are not in called genotypes.
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devteam
parents:
diff changeset
762 Loci which do not have any potential alternates have '.' for ALT.
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devteam
parents:
diff changeset
763
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devteam
parents:
diff changeset
764 Reporting::
2dd40b601766 Uploaded
devteam
parents:
diff changeset
765
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devteam
parents:
diff changeset
766 -P --pvar N Report sites if the probability that there is a polymorphism
2dd40b601766 Uploaded
devteam
parents:
diff changeset
767 at the site is greater than N. default: 0.0. Note that post-
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devteam
parents:
diff changeset
768 filtering is generally recommended over the use of this parameter.
2dd40b601766 Uploaded
devteam
parents:
diff changeset
769
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devteam
parents:
diff changeset
770 Population model::
2dd40b601766 Uploaded
devteam
parents:
diff changeset
771
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devteam
parents:
diff changeset
772 -T --theta N The expected mutation rate or pairwise nucleotide diversity
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devteam
parents:
diff changeset
773 among the population under analysis. This serves as the
2dd40b601766 Uploaded
devteam
parents:
diff changeset
774 single parameter to the Ewens Sampling Formula prior model
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devteam
parents:
diff changeset
775 default: 0.001
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devteam
parents:
diff changeset
776 -p --ploidy N Sets the default ploidy for the analysis to N. default: 2
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devteam
parents:
diff changeset
777 -J --pooled-discrete
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devteam
parents:
diff changeset
778 Assume that samples result from pooled sequencing.
2dd40b601766 Uploaded
devteam
parents:
diff changeset
779 Model pooled samples using discrete genotypes across pools.
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devteam
parents:
diff changeset
780 When using this flag, set --ploidy to the number of
2dd40b601766 Uploaded
devteam
parents:
diff changeset
781 alleles in each sample or use the --cnv-map to define
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devteam
parents:
diff changeset
782 per-sample ploidy.
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devteam
parents:
diff changeset
783 -K --pooled-continuous
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devteam
parents:
diff changeset
784 Output all alleles which pass input filters, regardles of
2dd40b601766 Uploaded
devteam
parents:
diff changeset
785 genotyping outcome or model.
2dd40b601766 Uploaded
devteam
parents:
diff changeset
786
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devteam
parents:
diff changeset
787 Reference allele::
2dd40b601766 Uploaded
devteam
parents:
diff changeset
788
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devteam
parents:
diff changeset
789 -Z --use-reference-allele
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devteam
parents:
diff changeset
790 This flag includes the reference allele in the analysis as
2dd40b601766 Uploaded
devteam
parents:
diff changeset
791 if it is another sample from the same population.
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devteam
parents:
diff changeset
792 --reference-quality MQ,BQ
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devteam
parents:
diff changeset
793 Assign mapping quality of MQ to the reference allele at each
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devteam
parents:
diff changeset
794 site and base quality of BQ. default: 100,60
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devteam
parents:
diff changeset
795
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parents:
diff changeset
796 Allele scope::
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parents:
diff changeset
797
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parents:
diff changeset
798 -I --no-snps Ignore SNP alleles.
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devteam
parents:
diff changeset
799 -i --no-indels Ignore insertion and deletion alleles.
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devteam
parents:
diff changeset
800 -X --no-mnps Ignore multi-nuceotide polymorphisms, MNPs.
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devteam
parents:
diff changeset
801 -u --no-complex Ignore complex events (composites of other classes).
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devteam
parents:
diff changeset
802 -n --use-best-n-alleles N
2dd40b601766 Uploaded
devteam
parents:
diff changeset
803 Evaluate only the best N SNP alleles, ranked by sum of
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devteam
parents:
diff changeset
804 supporting quality scores. (Set to 0 to use all; default: all)
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devteam
parents:
diff changeset
805 -E --max-complex-gap N
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devteam
parents:
diff changeset
806 --haplotype-length N
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devteam
parents:
diff changeset
807 Allow haplotype calls with contiguous embedded matches of up
2dd40b601766 Uploaded
devteam
parents:
diff changeset
808 to this length. (default: 3)
15
59731e950e23 Fix some options.
soranzo
parents: 13
diff changeset
809 --min-repeat-size N
13
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devteam
parents:
diff changeset
810 When assembling observations across repeats, require the total repeat
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devteam
parents:
diff changeset
811 length at least this many bp. (default: 5)
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devteam
parents:
diff changeset
812 --min-repeat-entropy N
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devteam
parents:
diff changeset
813 To detect interrupted repeats, build across sequence until it has
2dd40b601766 Uploaded
devteam
parents:
diff changeset
814 entropy > N bits per bp. (default: 0, off)
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devteam
parents:
diff changeset
815 --no-partial-observations
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devteam
parents:
diff changeset
816 Exclude observations which do not fully span the dynamically-determined
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devteam
parents:
diff changeset
817 detection window. (default, use all observations, dividing partial
2dd40b601766 Uploaded
devteam
parents:
diff changeset
818 support across matching haplotypes when generating haplotypes.)
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devteam
parents:
diff changeset
819
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parents:
diff changeset
820 Indel realignment::
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parents:
diff changeset
821
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devteam
parents:
diff changeset
822 -O --dont-left-align-indels
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devteam
parents:
diff changeset
823 Turn off left-alignment of indels, which is enabled by default.
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parents:
diff changeset
824
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parents:
diff changeset
825 Input filters::
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parents:
diff changeset
826
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devteam
parents:
diff changeset
827 -4 --use-duplicate-reads
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devteam
parents:
diff changeset
828 Include duplicate-marked alignments in the analysis.
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devteam
parents:
diff changeset
829 default: exclude duplicates marked as such in alignments
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devteam
parents:
diff changeset
830 -m --min-mapping-quality Q
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devteam
parents:
diff changeset
831 Exclude alignments from analysis if they have a mapping
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devteam
parents:
diff changeset
832 quality less than Q. default: 1
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devteam
parents:
diff changeset
833 -q --min-base-quality Q
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devteam
parents:
diff changeset
834 Exclude alleles from analysis if their supporting base
2dd40b601766 Uploaded
devteam
parents:
diff changeset
835 quality is less than Q. default: 0
2dd40b601766 Uploaded
devteam
parents:
diff changeset
836 -R --min-supporting-allele-qsum Q
2dd40b601766 Uploaded
devteam
parents:
diff changeset
837 Consider any allele in which the sum of qualities of supporting
2dd40b601766 Uploaded
devteam
parents:
diff changeset
838 observations is at least Q. default: 0
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devteam
parents:
diff changeset
839 -Y --min-supporting-mapping-qsum Q
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devteam
parents:
diff changeset
840 Consider any allele in which and the sum of mapping qualities of
2dd40b601766 Uploaded
devteam
parents:
diff changeset
841 supporting reads is at least Q. default: 0
2dd40b601766 Uploaded
devteam
parents:
diff changeset
842 -Q --mismatch-base-quality-threshold Q
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devteam
parents:
diff changeset
843 Count mismatches toward --read-mismatch-limit if the base
2dd40b601766 Uploaded
devteam
parents:
diff changeset
844 quality of the mismatch is >= Q. default: 10
2dd40b601766 Uploaded
devteam
parents:
diff changeset
845 -U --read-mismatch-limit N
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devteam
parents:
diff changeset
846 Exclude reads with more than N mismatches where each mismatch
2dd40b601766 Uploaded
devteam
parents:
diff changeset
847 has base quality >= mismatch-base-quality-threshold.
2dd40b601766 Uploaded
devteam
parents:
diff changeset
848 default: ~unbounded
2dd40b601766 Uploaded
devteam
parents:
diff changeset
849 -z --read-max-mismatch-fraction N
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devteam
parents:
diff changeset
850 Exclude reads with more than N [0,1] fraction of mismatches where
2dd40b601766 Uploaded
devteam
parents:
diff changeset
851 each mismatch has base quality >= mismatch-base-quality-threshold
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devteam
parents:
diff changeset
852 default: 1.0
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devteam
parents:
diff changeset
853 -$ --read-snp-limit N
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devteam
parents:
diff changeset
854 Exclude reads with more than N base mismatches, ignoring gaps
2dd40b601766 Uploaded
devteam
parents:
diff changeset
855 with quality >= mismatch-base-quality-threshold.
2dd40b601766 Uploaded
devteam
parents:
diff changeset
856 default: ~unbounded
2dd40b601766 Uploaded
devteam
parents:
diff changeset
857 -e --read-indel-limit N
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devteam
parents:
diff changeset
858 Exclude reads with more than N separate gaps.
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devteam
parents:
diff changeset
859 default: ~unbounded
2dd40b601766 Uploaded
devteam
parents:
diff changeset
860 -0 --standard-filters Use stringent input base and mapping quality filters
2dd40b601766 Uploaded
devteam
parents:
diff changeset
861 Equivalent to -m 30 -q 20 -R 0 -S 0
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devteam
parents:
diff changeset
862 -F --min-alternate-fraction N
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devteam
parents:
diff changeset
863 Require at least this fraction of observations supporting
2dd40b601766 Uploaded
devteam
parents:
diff changeset
864 an alternate allele within a single individual in the
2dd40b601766 Uploaded
devteam
parents:
diff changeset
865 in order to evaluate the position. default: 0.2
2dd40b601766 Uploaded
devteam
parents:
diff changeset
866 -C --min-alternate-count N
2dd40b601766 Uploaded
devteam
parents:
diff changeset
867 Require at least this count of observations supporting
2dd40b601766 Uploaded
devteam
parents:
diff changeset
868 an alternate allele within a single individual in order
2dd40b601766 Uploaded
devteam
parents:
diff changeset
869 to evaluate the position. default: 2
2dd40b601766 Uploaded
devteam
parents:
diff changeset
870 -3 --min-alternate-qsum N
2dd40b601766 Uploaded
devteam
parents:
diff changeset
871 Require at least this sum of quality of observations supporting
2dd40b601766 Uploaded
devteam
parents:
diff changeset
872 an alternate allele within a single individual in order
2dd40b601766 Uploaded
devteam
parents:
diff changeset
873 to evaluate the position. default: 0
2dd40b601766 Uploaded
devteam
parents:
diff changeset
874 -G --min-alternate-total N
2dd40b601766 Uploaded
devteam
parents:
diff changeset
875 Require at least this count of observations supporting
2dd40b601766 Uploaded
devteam
parents:
diff changeset
876 an alternate allele within the total population in order
2dd40b601766 Uploaded
devteam
parents:
diff changeset
877 to use the allele in analysis. default: 1
2dd40b601766 Uploaded
devteam
parents:
diff changeset
878 -! --min-coverage N
2dd40b601766 Uploaded
devteam
parents:
diff changeset
879 Require at least this coverage to process a site. default: 0
2dd40b601766 Uploaded
devteam
parents:
diff changeset
880
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devteam
parents:
diff changeset
881 Population priors::
2dd40b601766 Uploaded
devteam
parents:
diff changeset
882
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devteam
parents:
diff changeset
883 -k --no-population-priors
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devteam
parents:
diff changeset
884 Equivalent to --pooled-discrete --hwe-priors-off and removal of
2dd40b601766 Uploaded
devteam
parents:
diff changeset
885 Ewens Sampling Formula component of priors.
2dd40b601766 Uploaded
devteam
parents:
diff changeset
886
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devteam
parents:
diff changeset
887 Mappability priors::
2dd40b601766 Uploaded
devteam
parents:
diff changeset
888
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devteam
parents:
diff changeset
889 -w --hwe-priors-off
2dd40b601766 Uploaded
devteam
parents:
diff changeset
890 Disable estimation of the probability of the combination
2dd40b601766 Uploaded
devteam
parents:
diff changeset
891 arising under HWE given the allele frequency as estimated
2dd40b601766 Uploaded
devteam
parents:
diff changeset
892 by observation frequency.
2dd40b601766 Uploaded
devteam
parents:
diff changeset
893 -V --binomial-obs-priors-off
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894 Disable incorporation of prior expectations about observations.
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895 Uses read placement probability, strand balance probability,
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896 and read position (5'-3') probability.
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897 -a --allele-balance-priors-off
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898 Disable use of aggregate probability of observation balance between alleles
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899 as a component of the priors.
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900
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901 Genotype likelihoods::
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902
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903 --observation-bias FILE
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904 Read length-dependent allele observation biases from FILE.
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905 The format is [length] [alignment efficiency relative to reference]
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906 where the efficiency is 1 if there is no relative observation bias.
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907 --base-quality-cap Q
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908 Limit estimated observation quality by capping base quality at Q.
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909 --experimental-gls
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910 Generate genotype likelihoods using 'effective base depth' metric
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911 qual = 1-BaseQual * 1-MapQual. Incorporate partial observations.
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912 This is the default when contamination estimates are provided.
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913 Optimized for diploid samples.
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914 --prob-contamination F
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915 An estimate of contamination to use for all samples. default: 10e-9
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916 --contamination-estimates FILE
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917 A file containing per-sample estimates of contamination, such as
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918 those generated by VerifyBamID. The format should be:
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919 sample p(read=R|genotype=AR) p(read=A|genotype=AA)
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920 Sample '*' can be used to set default contamination estimates.
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921
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922 Algorithmic features::
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923
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924 --report-genotype-likelihood-max
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925 Report genotypes using the maximum-likelihood estimate provided
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926 from genotype likelihoods.
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927 -B --genotyping-max-iterations N
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928 Iterate no more than N times during genotyping step. default: 1000.
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929 --genotyping-max-banddepth N
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930 Integrate no deeper than the Nth best genotype by likelihood when
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931 genotyping. default: 6.
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932 -W --posterior-integration-limits N,M
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933 Integrate all genotype combinations in our posterior space
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934 which include no more than N samples with their Mth best
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935 data likelihood. default: 1,3.
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936 -N --exclude-unobserved-genotypes
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937 Skip sample genotypings for which the sample has no supporting reads.
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938 -S --genotype-variant-threshold N
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939 Limit posterior integration to samples where the second-best
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940 genotype likelihood is no more than log(N) from the highest
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941 genotype likelihood for the sample. default: ~unbounded
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942 -j --use-mapping-quality
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943 Use mapping quality of alleles when calculating data likelihoods.
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944 -H --harmonic-indel-quality
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945 Use a weighted sum of base qualities around an indel, scaled by the
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946 distance from the indel. By default use a minimum BQ in flanking sequence.
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947 -D --read-dependence-factor N
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948 Incorporate non-independence of reads by scaling successive
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949 observations by this factor during data likelihood
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950 calculations. default: 0.9
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951 -= --genotype-qualities
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952 Calculate the marginal probability of genotypes and report as GQ in
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953 each sample field in the VCF output.
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954
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955
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956 ------
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957
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958 **Acknowledgments**
13
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959
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960 The initial version of the wrapper was produced by Dan Blankenberg and upgraded by Anton Nekrutenko.
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961 TNG was developed by Bjoern Gruening
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962 </help>
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963 <expand macro="citations" />
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964 </tool>