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annotate freebayes.xml @ 32:8a7a42541080 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit cce7fcdd5e8ba8636c751f9f974bf07a6845ba1c"
author iuc
date Wed, 01 Dec 2021 21:50:06 +0000
parents 57def2d7c093
children 04fa42777df9
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8a7a42541080 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit cce7fcdd5e8ba8636c751f9f974bf07a6845ba1c"
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1 <tool id="freebayes" name="FreeBayes" version="@TOOL_VERSION@+galaxy0">
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2 <description>bayesian genetic variant detector</description>
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3 <xrefs>
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4 <xref type="bio.tools">freebayes</xref>
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5 </xrefs>
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6 <macros>
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7 <import>macros.xml</import>
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8 </macros>
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9 <expand macro="requirements">
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10 <requirement type="package" version="5.1.0">gawk</requirement>
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11 <requirement type="package" version="20211022">parallel</requirement>
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12 </expand>
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13 <command detect_errors="exit_code"><![CDATA[
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14 ##set up input files
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15
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16 #set $reference_fasta_filename = "localref.fa"
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17
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18 #if str( $reference_source.reference_source_selector ) == "history":
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19 ln -s -f '${reference_source.ref_file}' '${reference_fasta_filename}' &&
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20 samtools faidx '${reference_fasta_filename}' 2>&1 || echo "Error running samtools faidx for FreeBayes" >&2 &&
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21 #else:
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22 #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path )
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23 #end if
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25 #if $reference_source.batchmode.processmode == 'merge':
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26 #set $input_bamfiles = $reference_source.batchmode.input_bams
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27 #else:
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28 #set $input_bamfiles = [ $reference_source.batchmode.input_bams ]
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29 #end if
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31 #for $bam_count, $input_bam in enumerate( $input_bamfiles ):
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32 #if $input_bam.ext == 'bam':
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33 ln -s -f '${input_bam}' 'b_${bam_count}.bam' &&
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34 ln -s -f '${input_bam.metadata.bam_index}' 'b_${bam_count}.bam.bai' &&
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35 #elif $input_bam.ext == 'cram':
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36 ln -s -f '${input_bam}' 'b_${bam_count}.cram' &&
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37 ln -s -f '${input_bam.metadata.cram_index}' 'b_${bam_count}.cram.crai' &&
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38 #end if
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39 #end for
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41 ## Tabixize optional input_variant_vcf file (for --variant-input option)
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42 #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( $options_type.optional_inputs.input_variant_type.input_variant_type_selector ) == "provide_vcf":
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43 ln -s -f '${options_type.optional_inputs.input_variant_type.input_variant_vcf}' input_variant_vcf.vcf.gz &&
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44 ln -s -f '${Tabixized_input}' input_variant_vcf.vcf.gz.tbi &&
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45 #end if
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47 ##if the user has specified a region or target file, just use that instead of calculating a set of unique regions
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48 #if str( $target_limit_type.target_limit_type_selector ) == "limit_by_target_file":
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49 ln -s '${target_limit_type.input_target_bed}' regions_all.bed &&
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50 #elif str( $target_limit_type.target_limit_type_selector ) == "limit_by_region":
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51 printf '${target_limit_type.region_chromosome}\t${target_limit_type.region_start}\t${target_limit_type.region_end}' > regions_all.bed &&
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52 #else
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53 ##divide up the regions in the bam file for efficient processing
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54 #for $bam_count, $input_bam in enumerate( $input_bamfiles ):
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55 samtools view -H b_${bam_count}.${input_bam.ext}|
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56 grep '^@SQ' |
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57 cut -f 2- |
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58 awk '{ gsub("^SN:","",$1); gsub("^LN:","",$2); print $1"\t0\t"$2; }' >> regions_all.bed &&
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59 #end for
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60 #end if
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61
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62 sort -u regions_all.bed > regions_uniq.bed &&
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63 ## split into even small chunks, this has some disatvantages and will not be used for the moment
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64 ## bedtools makewindows -b regions_uniq.bed -w 10000000 -s 9990000 > regions.bed &&
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65
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66 mkdir vcf_output failed_alleles trace &&
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68 ## Finished setting up inputs
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70 for i in `cat regions_uniq.bed | awk '{print $1":"$2".."$3}'`;
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71 do
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72 echo "
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74 ## COMMAND LINE STARTS HERE
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76 freebayes
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78 --region '\$i'
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80 #for $bam_count, $input_bam in enumerate( $input_bamfiles ):
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81 --bam 'b_${bam_count}.${input_bam.ext}'
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82 #end for
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83 --fasta-reference '${reference_fasta_filename}'
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84
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85 ## Outputs
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86 --vcf './vcf_output/part_\$i.vcf'
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87
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88 ## Coverage
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89 #if str($coverage_options.coverage_options_selector) == "set":
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90 @COVERAGE@
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91 #end if
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92
25
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93 ##advanced options
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94 #if str( $options_type.options_type_selector ) == "simple":
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95 #pass
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96 #elif str( $options_type.options_type_selector ) == "simple_w_filters":
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97 --standard-filters
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98 #elif str( $options_type.options_type_selector ) == "naive":
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99 --haplotype-length 0
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100 --min-alternate-count 1
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101 --min-alternate-fraction 0.05
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102 --pooled-continuous
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103 --report-monomorphic
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104 #elif str( $options_type.options_type_selector ) == "naive_w_filters":
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105 --haplotype-length 0
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106 --min-alternate-count 1
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107 --min-alternate-fraction 0.05
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108 --pooled-continuous
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109 --report-monomorphic
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110 --standard-filters
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111 #elif str( $options_type.options_type_selector ) == "full":
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112 #if str( $options_type.optional_inputs.optional_inputs_selector ) == 'set':
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113 ${options_type.optional_inputs.report_monomorphic}
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114
25
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115 #if $options_type.optional_inputs.output_trace_option:
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116 --trace ./trace/part_'\$i'.txt
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117 #end if
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118 #if $options_type.optional_inputs.output_failed_alleles_option:
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119 --failed-alleles ./failed_alleles/part_'\$i'.bed
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120 #end if
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121 #if $options_type.optional_inputs.samples:
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122 --samples '${options_type.optional_inputs.samples}'
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123 #end if
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124 #if $options_type.optional_inputs.populations:
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125 --populations '${options_type.optional_inputs.populations}'
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126 #end if
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127 #if $options_type.optional_inputs.A:
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128 --cnv-map '${options_type.optional_inputs.A}'
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129 #end if
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130 #if str( $options_type.optional_inputs.input_variant_type.input_variant_type_selector ) == "provide_vcf":
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131 --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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132 ${options_type.optional_inputs.input_variant_type.only_use_input_alleles}
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133 #end if
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134 #if $options_type.optional_inputs.haplotype_basis_alleles:
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135 --haplotype-basis-alleles '${options_type.optional_inputs.haplotype_basis_alleles}'
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136 #end if
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137 #if $options_type.optional_inputs.observation_bias:
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138 --observation-bias '${options_type.optional_inputs.observation_bias}'
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139 #end if
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140 #if $options_type.optional_inputs.contamination_estimates:
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141 --contamination-estimates '${options_type.optional_inputs.contamination_estimates}'
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142 #end if
32
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143 $options_type.optional_inputs.trim_complex_tail
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144 #end if
23
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145
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146 ## REPORTING
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147 #if str( $options_type.reporting.reporting_selector ) == "set":
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148 --pvar ${options_type.reporting.pvar}
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149 #end if
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150 ## POPULATION MODEL
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151 #if str( $options_type.population_model.population_model_selector ) == "set":
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152 --theta ${options_type.population_model.T}
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153 --ploidy ${options_type.population_model.P}
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154 ${options_type.population_model.J}
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155 ${options_type.population_model.K}
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156 #end if
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157
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158 ## REFERENCE ALLELE
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159 #if str( $options_type.reference_allele.reference_allele_selector ) == "set":
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160 ${options_type.reference_allele.Z}
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161 --reference-quality '${options_type.reference_allele.reference_quality}'
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162 #end if
13
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163
25
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164 ## ALLELE SCOPE
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165 #if str( $options_type.allele_scope.allele_scope_selector ) == "set":
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166 ${options_type.allele_scope.I}
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167 ${options_type.allele_scope.i}
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168 ${options_type.allele_scope.X}
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169 ${options_type.allele_scope.u}
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170 ${options_type.allele_scope.no_partial_observations}
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171
28
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172 -n ${options_type.allele_scope.n}
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173
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174 --haplotype-length ${options_type.allele_scope.haplotype_length}
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175 --min-repeat-size ${options_type.allele_scope.min_repeat_length}
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176 --min-repeat-entropy ${options_type.allele_scope.min_repeat_entropy}
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177 #end if
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178
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179 ## REALIGNMENT
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180 ${options_type.O}
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181
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182 ##INPUT FILTERS
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183 #if str( $options_type.input_filters.input_filters_selector ) == "set":
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184 $standard_filters
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185 ${options_type.input_filters.use_duplicate_reads}
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186 --min-mapping-quality ${options_type.input_filters.min_mapping_quality}
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187 --min-base-quality ${options_type.input_filters.min_base_quality}
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188 --min-supporting-allele-qsum ${options_type.input_filters.min_supporting_allele_qsum}
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189 --min-supporting-mapping-qsum ${options_type.input_filters.min_supporting_mapping_qsum}
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190 #if str( $options_type.input_filters.mismatch_filters.mismatch_filters_selector ) == "set":
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191 --mismatch-base-quality-threshold ${options_type.input_filters.mismatch_filters.mismatch_base_quality_threshold}
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192 #if str($options_type.input_filters.mismatch_filters.read_mismatch_limit)
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193 --read-mismatch-limit ${options_type.input_filters.mismatch_filters.read_mismatch_limit}
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194 #end if
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195 --read-max-mismatch-fraction ${options_type.input_filters.mismatch_filters.read_max_mismatch_fraction}
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196 --read-snp-limit ${options_type.input_filters.mismatch_filters.read_snp_limit}
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197 #end if
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198 --read-indel-limit ${options_type.input_filters.read_indel_limit}
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199 --min-alternate-fraction ${options_type.input_filters.min_alternate_fraction}
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200 --min-alternate-qsum ${options_type.input_filters.min_alternate_qsum}
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201 --min-alternate-count ${options_type.input_filters.min_alternate_count}
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202 --min-alternate-total ${options_type.input_filters.min_alternate_total}
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203 #end if
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204
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205 ## POPULATION AND MAPPABILITY PRIORS
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206 #if str( $options_type.population_mappability_priors.population_mappability_priors_selector ) == "set":
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207 ${options_type.population_mappability_priors.k}
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208 ${options_type.population_mappability_priors.w}
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209 ${options_type.population_mappability_priors.V}
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210 ${options_type.population_mappability_priors.a}
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211 #end if
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212
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213 ## GENOTYPE LIKELIHOODS
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214 #if str( $options_type.genotype_likelihoods.genotype_likelihoods_selector ) == "set":
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215 ${$options_type.genotype_likelihoods.experimental_gls}
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216
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217 --base-quality-cap ${$options_type.genotype_likelihoods.base_quality_cap}
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218 --prob-contamination ${$options_type.genotype_likelihoods.prob_contamination}
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219 #end if
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220
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221 ## ALGORITHMIC FEATURES
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222 #if str( $options_type.algorithmic_features.algorithmic_features_selector ) == "set":
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223 -B '${options_type.algorithmic_features.B}'
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224 -W '${options_type.algorithmic_features.W}'
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225 -D '${options_type.algorithmic_features.D}'
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226
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227 #if str($options_type.algorithmic_features.genotype_variant_threshold)
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228 -S ${options_type.algorithmic_features.genotype_variant_threshold}
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229 #end if
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230
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231 ${options_type.algorithmic_features.N}
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232 ${options_type.algorithmic_features.j}
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233 ${options_type.algorithmic_features.H}
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234 ${options_type.algorithmic_features.genotype_qualities}
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235 ${options_type.algorithmic_features.report_genotype_likelihood_max}
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236
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237 --genotyping-max-banddepth ${options_type.algorithmic_features.genotyping_max_banddepth}
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238 #end if
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239 #end if
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240
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241 ";
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242 done > freebayes_commands.sh &&
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243
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244 cat freebayes_commands.sh |
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245 parallel --will-cite -j \${GALAXY_SLOTS:-1} &&
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246
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247 ## make VCF header
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248 grep "^#" "./vcf_output/part_\$i.vcf" > header.txt &&
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249
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250 for i in `cat regions_uniq.bed | awk '{print $1":"$2".."$3}'`;
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251 do
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252 ## if this fails then it bails out the script
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253 cat "./vcf_output/part_\$i.vcf" | grep -v "^#" || true
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254 ;
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255 done | sort -k1,1 -k2,2n -k5,5 -u | cat header.txt - > '${output_vcf}'
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256
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257 #if str( $options_type.options_type_selector ) == "full":
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258 #if str( $options_type.optional_inputs.optional_inputs_selector ) == 'set':
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259 #if $options_type.optional_inputs.output_failed_alleles_option:
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260 &&
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261 for i in `cat regions.bed | awk '{print $1":"$2".."$3}'`;
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262 do
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263 cat "./failed_alleles/part_\$i.bed"
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264 ;
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265 done > '${output_failed_alleles_bed}'
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266 #end if
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267
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268 #if $options_type.optional_inputs.output_trace_option:
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269 &&
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270 for i in `cat regions.bed | awk '{print $1":"$2".."$3}'`;
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271 do
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272 cat './trace/part_\$i.txt'
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273 ;
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274 done > '${output_trace}'
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275 #end if
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276 #end if
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277 #end if
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278 ]]></command>
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279
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280 <inputs>
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281 <conditional name="reference_source">
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282 <param name="reference_source_selector" type="select" label="Choose the source for the reference genome">
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283 <option value="cached">Locally cached</option>
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284 <option value="history">History</option>
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285 </param>
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286 <when value="cached">
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287 <expand macro="input_bam">
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288 <expand macro="validation" />
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289 </expand>
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290 <param name="ref_file" type="select" label="Using reference genome">
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291 <options from_data_table="fasta_indexes" />
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292 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input dataset"/>
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293 </param>
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294 </when>
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295 <when value="history"> <!-- FIX ME!!!! -->
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296 <expand macro="input_bam" />
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297 <param name="ref_file" type="data" format="fasta" label="Use the following dataset as the reference sequence"
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298 help="You can upload a FASTA sequence to the history and use it as reference" />
23
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299 </when>
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300 </conditional>
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301 <conditional name="target_limit_type">
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302 <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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303 <option value="do_not_limit" selected="true">Do not limit</option>
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304 <option value="limit_by_target_file">Limit by target file</option>
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305 <option value="limit_by_region">Limit to region</option>
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306 </param>
28
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307 <when value="do_not_limit" />
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308 <when value="limit_by_target_file">
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309 <param name="input_target_bed" argument="--targets" type="data" format="bed" label="Limit analysis to regions in this BED dataset" />
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310 </when>
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311 <when value="limit_by_region">
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312 <param name="region_chromosome" argument="--region" type="text" label="Region Chromosome" value="" /> <!--only once? -->
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313 <param name="region_start" type="integer" label="Region Start" value="" />
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314 <param name="region_end" type="integer" label="Region End" value="" />
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315 </when>
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316 </conditional>
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317 <conditional name="coverage_options">
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318 <param name="coverage_options_selector" type="select" label="Read coverage"
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319 help="Sets --min-coverage, --limit-coverage, and --skip-coverage">
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320 <option value="do_not_set" selected="true">Use defaults</option>
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321 <option value="set">Specify coverage options</option>
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322 </param>
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323 <when value="set">
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324 <expand macro="par_min_cov" />
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325 </when>
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326 <when value="do_not_set" />
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327 </conditional>
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328 <conditional name="options_type">
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329 <param name="options_type_selector" type="select" label="Choose parameter selection level"
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330 help="Select how much control over the freebayes run you need">
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331 <option value="simple" selected="true">1. Simple diploid calling</option>
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332 <option value="simple_w_filters">2. Simple diploid calling with filtering and coverage</option>
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333 <option value="naive">3. Frequency-based pooled calling</option>
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334 <option value="naive_w_filters">4. Frequency-based pooled calling with filtering and coverage</option>
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335 <option value="full">5. Full list of options</option>
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336 </param>
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337 <when value="full">
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338
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339 <conditional name="optional_inputs">
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340 <param name="optional_inputs_selector" type="select" label="Additional inputs"
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341 help="Sets --samples, --populations, --cnv-map, --trace, --failed-alleles, --variant-input, --only-use-input-alleles, --haplotype-basis-alleles, --report-all-haplotype-alleles, --report-monomorphic options, --observation-bias, --contamination-estimates and --trim-complex-tail">
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342 <option value="do_not_set" selected="true">Do not provide additional inputs</option>
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343 <option value="set">Provide additional inputs</option>
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344 </param>
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345 <when value="set">
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346 <param name="output_failed_alleles_option" argument="--failed-alleles" type="boolean" truevalue="--failed-alleles" falsevalue="" checked="false"
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347 label="Write out failed alleles file" />
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348 <param name="output_trace_option" argument="--trace" type="boolean" truevalue="--trace" falsevalue="" checked="false"
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349 label="Write out algorithm trace file" />
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350 <param argument="--samples" type="data" format="txt"
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351 label="Limit analysis to samples listed (one per line) in this dataset" optional="true"
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352 help="By default FreeBayes will analyze all samples in its input BAM datasets" />
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353 <param argument="--populations" type="data" format="txt" optional="true"
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354 label="Populations dataset"
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355 help="Each line of this dataset should list a sample and a population which it is part of. The population-based bayesian inference model will then be partitioned on the basis of the populations" />
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356 <param name="A" argument="--cnv-map" type="data" format="bed" optional="true"
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357 label="Read a copy number map from a BED dataset"
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358 help="The BED dataset should have the format: '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. If not specified, copy number is set to as specified by --ploidy" />
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359 <conditional name="input_variant_type">
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360 <param name="input_variant_type_selector" type="select" label="Provide variants dataset">
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361 <option value="do_not_provide" selected="true">Do not provide</option>
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362 <option value="provide_vcf">Provide VCF dataset</option>
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363 </param>
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364 <when value="do_not_provide" />
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365 <when value="provide_vcf">
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366 <param name="input_variant_vcf" argument="--variant-input" type="data" format="vcf_bgzip"
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367 label="Use variants reported in this VCF dataset as input to the algorithm">
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368 <conversion name="Tabixized_input" type="tabix" />
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369 </param>
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370 <param name="only_use_input_alleles" argument="--only-use-input-alleles" type="boolean" truevalue="--only-use-input-alleles" falsevalue="" checked="false"
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371 label="Only provide variant calls and genotype likelihoods for sites in VCF" />
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372 </when>
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373 </conditional>
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374 <param name="haplotype_basis_alleles" argument="--haplotype-basis-alleles" type="data" format="vcf" optional="true"
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375 label="Only use variant alleles provided in this input VCF for the construction of complex or haplotype alleles" />
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376 <param name="report_monomorphic" argument="--report-monomorphic" type="boolean" truevalue="--report-monomorphic" falsevalue="" checked="false"
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377 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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378 <param name="observation_bias" argument="--observation-bias" type="data" format="tabular" optional="true"
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379 label="Load read length-dependent allele observation biases from"
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380 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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381 <param name="contamination_estimates" argument="--contamination-estimates" type="data" format="tabular" optional="true"
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382 label="Upload per-sample estimates of contamination from"
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383 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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384 <param name="trim_complex_tail" argument="--trim-complex-tail" type="boolean" truevalue="--trim-complex-tail" falsevalue=""
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385 label="Trim trailing reference matches" />
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386 </when>
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387 <when value="do_not_set" />
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388 </conditional>
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389
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diff changeset
390 <!-- reporting -->
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391 <conditional name="reporting">
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392 <param name="reporting_selector" type="select" label="Reporting options" help="Sets -P --pvar option">
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393 <option value="do_not_set" selected="true">Use defaults</option>
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394 <option value="set">Set reporting options</option>
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395 </param>
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396 <when value="set">
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397 <param argument="--pvar" type="float" value="0.0"
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398 label="Report sites if the probability that there is a polymorphism at the site is greater than"
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399 help="Note that post-filtering is generally recommended over the use of this parameter" />
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400 </when>
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401 <when value="do_not_set" />
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402 </conditional>
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403
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404 <!-- population model -->
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405 <conditional name="population_model">
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406 <param name="population_model_selector" type="select" label="Population model options"
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407 help="Sets --theta, --ploidy, --pooled-discrete, and --pooled-continuous options">
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408 <option value="do_not_set" selected="true">Use defaults</option>
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409 <option value="set">Set population model options</option>
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410 </param>
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411 <when value="set">
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412 <param name="T" argument="--theta" type="float" value="0.001"
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413 label="The expected mutation rate or pairwise nucleotide diversity among the population under analysis"
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414 help="This serves as the single parameter to the Ewens Sampling Formula prior model" />
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415 <param name="P" argument="--ploidy" type="integer" value="2"
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416 label="Set ploidy for the analysis" />
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417 <param name="J" argument="--pooled-discrete" type="boolean" truevalue="-J" falsevalue="" checked="false"
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418 label="Assume that samples result from pooled sequencing"
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419 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" />
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420 <param name="K" argument="--poled-continuous" type="boolean" truevalue="-K" falsevalue="" checked="false"
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421 label="Output all alleles which pass input filters, regardles of genotyping outcome or model" />
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422 </when>
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423 <when value="do_not_set" />
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424 </conditional>
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425
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diff changeset
426 <!-- reference allele -->
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427 <conditional name="reference_allele">
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428 <param name="reference_allele_selector" type="select" label="Reference allele options"
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429 help="Sets --use-reference-allele and --reference-quality options">
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430 <option value="do_not_set" selected="true">Use defaults</option>
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431 <option value="set">Set reference allele options</option>
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diff changeset
432 </param>
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433 <when value="set">
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434 <param name="Z" argument="--use-reference-allele" type="boolean" truevalue="-Z" falsevalue="" checked="false"
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435 label="Include the reference allele in the analysis as if it is another sample from the same population" />
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436 <param name="reference_quality" argument="--reference-quality" type="text" value="100,60"
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437 label="Assign mapping quality of MQ (100) to the reference allele at each site and base quality of BQ (60)" />
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438 </when>
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439 <when value="do_not_set" />
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440 </conditional>
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441
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442 <!-- allelic scope -->
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443 <conditional name="allele_scope">
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444 <param name="allele_scope_selector" type="select" label="Allelic scope options"
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445 help="Sets -I, i, -X, -u, -n, --haplotype-length, --min-repeat-size, --min-repeat-entropy, and --no-partial-observations options">
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446 <option value="do_not_set" selected="true">Use defaults</option>
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447 <option value="set">Set alleic scope options</option>
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448 </param>
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449 <when value="set">
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450 <param name="I" argument="--no-snps" type="boolean" truevalue="-I" falsevalue="" checked="false"
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451 label="Ignore SNP alleles" />
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452 <param name="i" argument="--no-indels" type="boolean" truevalue="-i" falsevalue="" checked="false"
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453 label="Ignore indels alleles" />
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454 <param name="X" argument="--no-mnps" type="boolean" truevalue="-X" falsevalue="" checked="false"
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parents: 27
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455 label="Ignore multi-nucleotide polymorphisms, MNPs" />
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456 <param name="u" argument="--no-complex" type="boolean" truevalue="-u" falsevalue="" checked="false"
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457 label="Ignore complex events (composites of other classes)" />
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458 <param name="n" argument="--use-best-n-alleles" type="integer" value="0"
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parents: 27
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459 label="How many best SNP alleles to evaluate"
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460 help="Alleles are ranked by the sum of supporting quality scores. Set to 0 to evaluate all" />
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461 <param name="haplotype_length" argument="--haplotype-length" type="integer" value="3"
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462 label="Allow haplotype calls with contiguous embedded matches of up to (nucleotides)" />
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parents: 27
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463 <param name="min_repeat_length" argument="--min-repeat-size" type="integer" value="5"
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464 label="When assembling observations across repeats, require the total repeat length at least this many bp" />
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465 <param name="min_repeat_entropy" argument="--min-repeat-entropy" type="integer" value="1"
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466 label="To detect interrupted repeats, build across sequence until it has entropy > (bits per bp)" />
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467 <param name="no_partial_observations" argument="--no-partial-observations" type="boolean" truevalue="--no-partial-observations" falsevalue="" checked="false"
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468 label="Exclude observations which do not fully span the dynamically-determined detection window"
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469 help="By default, FreeBayes uses all observations, dividing partial support across matching haplotypes when generating haplotypes" />
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470 </when>
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471 <when value="do_not_set" />
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472 </conditional>
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473
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474 <!-- indel realignment -->
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475 <param name="O" argument="--dont-left-align-indels" type="boolean" truevalue="-O" falsevalue="" checked="false"
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476 label="Turn off left-alignment of indels" />
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parents: 24
diff changeset
477
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parents: 22
diff changeset
478 <!-- input filters -->
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479 <conditional name="input_filters">
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480 <param name="input_filters_selector" type="select" label="Input filters">
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diff changeset
481 <option value="do_not_set" selected="true">No input filters (default)</option>
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482 <option value="set">Set input filters</option>
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diff changeset
483 </param>
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484 <when value="set">
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485 <param argument="--standard-filters" type="boolean" truevalue="--standard-filters" falsevalue="" checked="false"
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486 label="Use stringent input base and mapping quality filters"
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487 help="--min-mapping-quality 30 --min-base-quality 20, --min-supporting-allele-qsum 0 --genotype-variant-threshold 0"/>
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488 <param argument="--use-duplicate-reads" type="boolean" truevalue="--use-duplicate-reads" falsevalue="" checked="false"
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489 label="Include duplicate-marked alignments in the analysis" />
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490 <param argument="--min-mapping-quality" type="integer" value="1"
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diff changeset
491 label="Exclude alignments from analysis if they have a mapping quality less than" />
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492 <param argument="--min-base-quality" type="integer" value="0"
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diff changeset
493 label="Exclude alleles from analysis if their supporting base quality less than" />
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494 <param argument="--min-supporting-allele-qsum" type="integer" value="0"
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495 label="Consider any allele in which the sum of qualities of supporting observations is at least" />
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496 <param argument="--min-supporting-mapping-qsum" type="integer" value="0"
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diff changeset
497 label="Consider any allele in which and the sum of mapping qualities of supporting reads is at least" />
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diff changeset
498 <conditional name="mismatch_filters">
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499 <param name="mismatch_filters_selector" type="select" label="Mismatch filters"
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diff changeset
500 help="Sets -Q, -U, -z, and &#36; options">
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diff changeset
501 <option value="do_not_set" selected="true">No mismatch filters (default)</option>
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502 <option value="set">Set mismatch filters</option>
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diff changeset
503 </param>
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504 <when value="set">
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diff changeset
505 <param argument="--mismatch-base-quality-threshold" type="integer" value="10"
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diff changeset
506 label="Count mismatches toward -U (option below) if the base quality of the mismatch is >=" />
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diff changeset
507 <param argument="--read-mismatch-limit" type="integer" value="1000" optional="true"
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diff changeset
508 label="Exclude reads with more than N mismatches where each mismatch has base quality >= mismatch-base-quality-threshold (option above)"
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diff changeset
509 help="default=~unbounded" />
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diff changeset
510 <param argument="--read-max-mismatch-fraction" type="float" value="1.0" min="0.0" max="1.0"
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diff changeset
511 label="Exclude reads with more than N [0,1] fraction of mismatches where each mismatch has base quality >= mismatch-base-quality-threshold (second option above)" />
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diff changeset
512 <param name="read_snp_limit" argument="--read-snp-limit" type="integer" value="1000"
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diff changeset
513 label="Exclude reads with more than N base mismatches, ignoring gaps with quality >= mismatch-base-quality-threshold (third option above)"
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diff changeset
514 help="default=~unbounded" />
23
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diff changeset
515 </when>
28
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parents: 27
diff changeset
516 <when value="do_not_set" />
23
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diff changeset
517 </conditional>
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diff changeset
518 <param argument="--read-indel-limit" type="integer" value="1000"
28
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parents: 27
diff changeset
519 label="Exclude reads with more than this number of separate gaps"
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parents: 27
diff changeset
520 help="default=~unbounded" />
31
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diff changeset
521 <param argument="--min-alternate-fraction" type="float" value="0.05"
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parents: 27
diff changeset
522 label="Require at least this fraction of observations supporting an alternate allele within a single individual in the in order to evaluate the position" />
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parents: 30
diff changeset
523 <param argument="--min-alternate-qsum" type="integer" value="0"
57def2d7c093 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 3b5abd63372c2806870627e9dc2a2f0f52f2e52a"
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parents: 30
diff changeset
524 label="Require at least this sum of quality of observations supporting an alternate allele within a single individual in order to evaluate the position" />
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parents: 30
diff changeset
525 <param argument="--min-alternate-count" type="integer" value="2"
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parents: 27
diff changeset
526 label="Require at least this count of observations supporting an alternate allele within a single individual in order to evaluate the position" />
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parents: 30
diff changeset
527 <param argument="--min-alternate-total" type="integer" value="1"
28
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parents: 27
diff changeset
528 label="Require at least this count of observations supporting an alternate allele within the total population in order to use the allele in analysis" />
23
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parents: 22
diff changeset
529 </when>
28
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parents: 27
diff changeset
530 <when value="do_not_set" />
23
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parents: 22
diff changeset
531 </conditional>
25
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parents: 24
diff changeset
532
23
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parents: 22
diff changeset
533 <!-- population and mappability priors -->
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diff changeset
534 <conditional name="population_mappability_priors">
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parents: 22
diff changeset
535 <param name="population_mappability_priors_selector" type="select" label="Population and mappability priors"
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diff changeset
536 help="Sets -k, -w, -V, and -a options">
23
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diff changeset
537 <option value="do_not_set" selected="true">Use defaults</option>
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parents: 22
diff changeset
538 <option value="set">Set population and mappability priors</option>
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parents: 22
diff changeset
539 </param>
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diff changeset
540 <when value="set">
28
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parents: 27
diff changeset
541 <param name="k" argument="--no-population-priors" type="boolean" truevalue="-k" falsevalue="" checked="false"
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parents: 27
diff changeset
542 label="No population priors"
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parents: 27
diff changeset
543 help="Equivalent to --pooled-discrete --hwe-priors-off and removal of Ewens Sampling Formula component of priors" />
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parents: 27
diff changeset
544 <param name="w" argument="--hwe-priors-off" type="boolean" truevalue="-w" falsevalue="" checked="false"
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parents: 27
diff changeset
545 label="Disable estimation of the probability of the combination arising under HWE given the allele frequency as estimated by observation frequency" />
977a5301b66d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 27
diff changeset
546 <param name="V" argument="--binomial-obs-priors-off" type="boolean" truevalue="-V" falsevalue="" checked="false"
977a5301b66d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 27
diff changeset
547 label="Disable incorporation of prior expectations about observations"
977a5301b66d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
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parents: 27
diff changeset
548 help="Uses read placement probability, strand balance probability, and read position (5&#39;'-3&#39;') probability" />
977a5301b66d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
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parents: 27
diff changeset
549 <param name="a" argument="--allele-balance-priors-off" type="boolean" truevalue="-a" falsevalue="" checked="false"
977a5301b66d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
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parents: 27
diff changeset
550 label="Disable use of aggregate probability of observation balance between alleles as a component of the priors" />
23
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parents: 22
diff changeset
551 </when>
28
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parents: 27
diff changeset
552 <when value="do_not_set" />
23
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parents: 22
diff changeset
553 </conditional>
25
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parents: 24
diff changeset
554
23
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parents: 22
diff changeset
555 <!-- 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
556 <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
557 <param name="genotype_likelihoods_selector" type="select" label="Genotype likelihood options"
28
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parents: 27
diff changeset
558 help="Sets --base-quality-cap, --experimental-gls, and --prob-contamination options">
23
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parents: 22
diff changeset
559 <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
560 <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
561 </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
562 <when value="set">
28
977a5301b66d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 27
diff changeset
563 <param name="base_quality_cap" argument="--base-quality-cap" type="integer" value="0"
977a5301b66d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
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parents: 27
diff changeset
564 label="Limit estimated observation quality by capping base quality at" />
977a5301b66d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
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parents: 27
diff changeset
565 <param name="experimental_gls" argument="--experimental-gls" type="boolean" truevalue="--experimental-gls" falsevalue="" checked="false"
25
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parents: 24
diff changeset
566 label="Generate genotype likelihoods using 'effective base depth' metric qual = 1-BaseQual * 1-MapQual"
28
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iuc
parents: 27
diff changeset
567 help="Incorporate partial observations. This is the default when contamination estimates are provided. Optimized for diploid samples" />
977a5301b66d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 27
diff changeset
568 <param name="prob_contamination" argument="--prob-contamination" type="float" value="10e-9"
977a5301b66d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 27
diff changeset
569 label="An estimate of contamination to use for all samples" />
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
570 </when>
28
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parents: 27
diff changeset
571 <when value="do_not_set" />
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
572 </conditional>
25
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parents: 24
diff changeset
573
23
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parents: 22
diff changeset
574 <!-- algorithmic features -->
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parents: 22
diff changeset
575 <conditional name="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
576 <param name="algorithmic_features_selector" type="select" label="Algorithmic features"
25
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parents: 24
diff changeset
577 help="Sets --report-genotypes-likelihood-max, -B, --genotyping-max-banddepth, -W, -N, S, -j, -H, -D, -= options">
23
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parents: 22
diff changeset
578 <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
579 <option value="set">Set algorithmic features</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
580 </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
581 <when value="set">
28
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parents: 27
diff changeset
582 <param name="report_genotype_likelihood_max" argument="--report-genotype-likelihood-max" type="boolean" truevalue="--report-genotype-likelihood-max" falsevalue="" checked="false"
977a5301b66d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
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parents: 27
diff changeset
583 label="Report genotypes using the maximum-likelihood estimate provided from genotype likelihoods" />
977a5301b66d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
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parents: 27
diff changeset
584 <param name="B" argument="--genotyping-max-iterations" type="integer" value="1000"
977a5301b66d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
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parents: 27
diff changeset
585 label="Iterate no more than N times during genotyping step" />
977a5301b66d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 27
diff changeset
586 <param name="genotyping_max_banddepth" argument="--genotyping-max-banddepth" type="integer" value="6"
977a5301b66d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 27
diff changeset
587 label="Integrate no deeper than the Nth best genotype by likelihood when genotyping" />
977a5301b66d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
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parents: 27
diff changeset
588 <param name="W" argument="--posterior-integration-limits" type="text" value="1,3"
977a5301b66d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 27
diff changeset
589 label="Integrate all genotype combinations in our posterior space which include no more than N (1) samples with their Mth (3) best data likelihood" />
977a5301b66d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
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parents: 27
diff changeset
590 <param name="N" argument="--exclude-unobserved-genotypes" type="boolean" truevalue="--exclude-unobserved-genotypes" falsevalue="" checked="false"
977a5301b66d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
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parents: 27
diff changeset
591 label="Skip sample genotypings for which the sample has no supporting reads" />
977a5301b66d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 27
diff changeset
592 <param name="genotype_variant_threshold" argument="--genotype-variant-threshold" type="integer" value="" optional="true"
977a5301b66d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 27
diff changeset
593 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"
977a5301b66d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 27
diff changeset
594 help="default=~unbounded" />
977a5301b66d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
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parents: 27
diff changeset
595 <param name="j" argument="--use-mapping-quality" type="boolean" truevalue="-j" falsevalue="" checked="false"
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diff changeset
596 label="Use mapping quality of alleles when calculating data likelihoods" />
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parents: 27
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597 <param name="H" argument="--harmonic-indel-quality" type="boolean" truevalue="-H" falsevalue="" checked="false"
25
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diff changeset
598 label="Use a weighted sum of base qualities around an indel, scaled by the distance from the indel"
28
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parents: 27
diff changeset
599 help="By default, FreeBayes uses a minimum Base Quality in flanking sequence" />
977a5301b66d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
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parents: 27
diff changeset
600 <param name="D" argument="--read-dependence-factor" type="float" value="0.9"
977a5301b66d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
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parents: 27
diff changeset
601 label="Incorporate non-independence of reads by scaling successive observations by this factor during data likelihood calculations" />
977a5301b66d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
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parents: 27
diff changeset
602 <param name="genotype_qualities" argument="--genotype-qualities" type="boolean" truevalue="--genotype-qualities" falsevalue="" checked="false"
977a5301b66d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 27
diff changeset
603 label="Calculate the marginal probability of genotypes and report as GQ in each sample field in the VCF output" />
23
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diff changeset
604 </when>
28
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parents: 27
diff changeset
605 <when value="do_not_set" />
23
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diff changeset
606 </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
607 </when>
28
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diff changeset
608 <when value="simple" />
30
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diff changeset
609 <when value="simple_w_filters" />
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
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610 <when value="naive" />
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
611 <when value="naive_w_filters" />
23
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parents: 22
diff changeset
612 </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
613 </inputs>
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
614 <outputs>
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 22
diff changeset
615 <data format="vcf" name="output_vcf" label="${tool.name} on ${on_string} (variants)" />
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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diff changeset
616 <data format="bed" name="output_failed_alleles_bed" label="${tool.name} on ${on_string} (failed alleles)">
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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parents: 22
diff changeset
617 <filter>( options_type['options_type_selector'] == 'cline' or options_type['options_type_selector'] == 'full' ) and options_type['optional_inputs']['optional_inputs_selector'] == 'set' and options_type['optional_inputs']['output_failed_alleles_option'] is True</filter>
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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diff changeset
618 </data>
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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parents: 22
diff changeset
619 <data format="txt" name="output_trace" label="${tool.name} on ${on_string} (trace)">
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
620 <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>
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
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diff changeset
621 </data>
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
622 </outputs>
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
623 <tests>
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 22
diff changeset
624 <test>
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
625 <param name="reference_source_selector" value="history" />
27
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iuc
parents: 26
diff changeset
626 <param name="processmode" value="individual" />
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
627 <param name="ref_file" ftype="fasta" value="freebayes-phix174.fasta"/>
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 22
diff changeset
628 <param name="input_bams" ftype="bam" value="freebayes-phix174.bam"/>
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 22
diff changeset
629 <param name="options_type_selector" value="simple"/>
29
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iuc
parents: 28
diff changeset
630 <output name="output_vcf" file="freebayes-phix174-test1.vcf" lines_diff="4" />
23
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parents: 22
diff changeset
631 </test>
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 22
diff changeset
632 <test>
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 22
diff changeset
633 <param name="reference_source_selector" value="history" />
27
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iuc
parents: 26
diff changeset
634 <param name="processmode" value="individual" />
23
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 22
diff changeset
635 <param name="ref_file" ftype="fasta" value="freebayes-phix174.fasta"/>
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 22
diff changeset
636 <param name="input_bams" ftype="bam" value="freebayes-phix174.bam"/>
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 22
diff changeset
637 <param name="options_type_selector" value="naive_w_filters"/>
30
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
638 <param name="coverage_options_selector" value="set" />
23
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 22
diff changeset
639 <param name="min_coverage" value="14"/>
29
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iuc
parents: 28
diff changeset
640 <output name="output_vcf" file="freebayes-phix174-test2.vcf" lines_diff="4" />
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
641 </test>
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 22
diff changeset
642 <test>
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 22
diff changeset
643 <param name="reference_source_selector" value="history" />
27
9f164587a92f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit d2f9b1728a6525b599e2c014a183b0415b27a870
iuc
parents: 26
diff changeset
644 <param name="processmode" value="individual" />
23
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 22
diff changeset
645 <param name="ref_file" ftype="fasta" value="freebayes-phix174.fasta"/>
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 22
diff changeset
646 <param name="input_bams" ftype="bam" value="freebayes-phix174.bam"/>
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 22
diff changeset
647 <param name="options_type_selector" value="naive_w_filters"/>
30
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iuc
parents: 29
diff changeset
648 <param name="coverage_options_selector" value="set" />
23
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 22
diff changeset
649 <param name="min_coverage" value="14"/>
29
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parents: 28
diff changeset
650 <output name="output_vcf" file="freebayes-phix174-test3.vcf" lines_diff="4" />
23
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 22
diff changeset
651 </test>
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 22
diff changeset
652 <test>
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 22
diff changeset
653 <param name="reference_source_selector" value="history" />
27
9f164587a92f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit d2f9b1728a6525b599e2c014a183b0415b27a870
iuc
parents: 26
diff changeset
654 <param name="processmode" value="individual" />
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
655 <param name="ref_file" ftype="fasta" value="freebayes-phix174.fasta"/>
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
656 <param name="input_bams" ftype="bam" value="freebayes-phix174.bam"/>
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
657 <param name="options_type_selector" value="full"/>
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
658 <param name="population_model_selector" value="set"/>
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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diff changeset
659 <param name="P" value="1"/>
32
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iuc
parents: 31
diff changeset
660 <param name="trim_complex_tail" value="--trim-complex-tail"/>
29
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parents: 28
diff changeset
661 <output name="output_vcf" file="freebayes-phix174-test4.vcf" lines_diff="4" />
23
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diff changeset
662 </test>
30
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parents: 29
diff changeset
663 <test>
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
664 <param name="reference_source_selector" value="history" />
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
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parents: 29
diff changeset
665 <param name="processmode" value="individual" />
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
666 <param name="ref_file" ftype="fasta" value="freebayes-hxb2.fasta"/>
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
667 <param name="input_bams" ftype="bam" value="freebayes-hxb2.bam"/>
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
668 <param name="options_type_selector" value="simple"/>
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
669 <param name="coverage_options_selector" value="set" />
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
670 <param name="min_coverage" value="250" />
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
671 <output name="output_vcf" file="freebayes-hxb2-test5.vcf" lines_diff="4" />
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
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diff changeset
672 </test>
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
673 <test>
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
674 <param name="reference_source_selector" value="history" />
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
675 <param name="processmode" value="individual" />
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
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676 <param name="ref_file" ftype="fasta" value="freebayes-hxb2.fasta"/>
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677 <param name="input_bams" ftype="bam" value="freebayes-hxb2.bam"/>
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678 <param name="options_type_selector" value="simple"/>
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679 <param name="coverage_options_selector" value="set" />
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680 <param name="limit_coverage" value="400" />
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681 <output name="output_vcf" file="freebayes-hxb2-test6.vcf" lines_diff="4" />
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682 </test>
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683 <test>
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684 <param name="reference_source_selector" value="history" />
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685 <param name="processmode" value="individual" />
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686 <param name="ref_file" ftype="fasta" value="freebayes-hxb2.fasta"/>
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687 <param name="input_bams" ftype="bam" value="freebayes-hxb2.bam"/>
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688 <param name="options_type_selector" value="simple"/>
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689 <param name="coverage_options_selector" value="set" />
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690 <param name="skip_coverage" value="100" />
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691 <output name="output_vcf" file="freebayes-hxb2-test7.vcf" lines_diff="4" />
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692 </test>
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693 <test> <!-- Test with CRAM -->
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694 <param name="reference_source_selector" value="history" />
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695 <param name="processmode" value="individual" />
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696 <param name="ref_file" ftype="fasta" value="freebayes-phix174.fasta"/>
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697 <param name="input_bams" ftype="cram" value="freebayes-phix174.cram"/>
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698 <param name="options_type_selector" value="simple"/>
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699 <output name="output_vcf" file="freebayes-phix174-test1.vcf" lines_diff="4" />
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700 </test>
23
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701 </tests>
30
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702 <help><![CDATA[
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703 **What it does**
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704
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705 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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706
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707 See https://github.com/ekg/freebayes for details on FreeBayes.
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708
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709 ------
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710
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711 **Description**
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712
28
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713 Provided some BAM dataset(s) and a reference sequence, FreeBayes will produce a VCF dataset describing SNPs, indels, and complex variants in samples in the input alignments.
13
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714
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715 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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716
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717 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.
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718
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719 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.
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720
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721 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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722
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723 -------
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724
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725 **Galaxy-specific options**
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726
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727 Galaxy allows five levels of control over FreeBayes options, provided by the **Choose parameter selection level** menu option. These are:
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728
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729 1. *Simple diploid calling*: The simplest possible FreeBayes application. Equivalent to using FreeBayes with only a BAM input and no other parameter options.
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730 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-variant-threshold 0) and --min-coverage.
977a5301b66d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
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731 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 variants in mixtures such as viral, bacterial, or organellar genomes.
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732 4. *Frequency-based pooled calling with filtering and coverage*: Same as #3 but adds -0 and --min-coverage like in #2.
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733 5. *Complete list of all options*: Gives you full control by exposing all FreeBayes options as Galaxy parameters.
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734
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735 ------
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736
30
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737 **Command-line parameters**
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738
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739 **Input**::
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740
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741 --bam FILE The file or set of BAM files to be analyzed.
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742 --bam-list FILE A file containing a list of BAM files to be analyzed.
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743
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744 --stdin Read BAM input on stdin.
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
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745 --fasta-reference FILE Use FILE as the reference sequence for analysis.
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
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746 An index file (FILE.fai) will be created if none exists.
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747 If neither --targets nor --region are specified, FreeBayes
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
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748 will analyze every position in this reference.
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
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749 --targets FILE Limit analysis to targets listed in the BED-format FILE.
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
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750 --region <chrom>:<start>-<end> Limit analysis to the specified region, 0-base coordinates,
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
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751 end_position not included (same as BED format).
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
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752 Either '-' or '..' maybe used as a separator.
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
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753 --samples FILE Limit analysis to samples listed (one per line) in the FILE.
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754 By default FreeBayes will analyze all samples in its input
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
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755 BAM files.
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756 --populations FILE Each line of FILE should list a sample and a population which
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
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757 it is part of. The population-based bayesian inference model
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
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758 will then be partitioned on the basis of the populations.
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759 --cnv-map FILE Read a copy number map from the BED file FILE, which has
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760 either a sample-level ploidy:
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
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761 sample_name copy_number
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762 or a region-specific format:
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763 seq_name start end sample_name copy_number
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764 ... for each region in each sample which does not have the
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765 default copy number as set by --ploidy. These fields can be delimited
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
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766 by space or tab.
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767
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768 **Output**::
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769
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770 --vcf FILE Output VCF-format results to FILE. (default: stdout)
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771 --gvcf Write gVCF output, which indicates coverage in uncalled regions.
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diff changeset
772 --gvcf-chunk NUM When writing gVCF output emit a record for every NUM bases.
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
773 --gvcf-dont-use-chunk When writing the gVCF output emit a record for all bases if
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
774 set to "true" , will also route an int to --gvcf-chunk
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
775 similar to --output-mode EMIT_ALL_SITES from GATK
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
776 --variant-input VCF Use variants reported in VCF file as input to the algorithm.
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
777 Variants in this file will included in the output even if
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
778 there is not enough support in the data to pass input filters.
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
779 --only-use-input-alleles Only provide variant calls and genotype likelihoods for sites
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
780 and alleles which are provided in the VCF input, and provide
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
781 output in the VCF for all input alleles, not just those which
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
782 have support in the data.
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
783 --haplotype-basis-alleles VCF When specified, only variant alleles provided in this input
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
784 VCF will be used for the construction of complex or haplotype
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
785 alleles.
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
786 --report-all-haplotype-alleles At sites where genotypes are made over haplotype alleles,
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
787 provide information about all alleles in output, not only
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
788 those which are called.
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
789 --report-monomorphic Report even loci which appear to be monomorphic, and report all
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
790 considered alleles, even those which are not in called genotypes.
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
791 Loci which do not have any potential alternates have '.' for ALT.
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
792 --pvar N Report sites if the probability that there is a polymorphism
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
793 at the site is greater than N. default: 0.0. Note that post-
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
794 filtering is generally recommended over the use of this parameter.
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
795 --strict-vcf Generate strict VCF format (FORMAT/GQ will be an int)
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
796
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
797 **Population model**::
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
798
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
799 --theta N The expected mutation rate or pairwise nucleotide diversity
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
800 among the population under analysis. This serves as the
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
801 single parameter to the Ewens Sampling Formula prior model
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
802 default: 0.001
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
803 --ploidy N Sets the default ploidy for the analysis to N. default: 2
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
804 --pooled-discrete Assume that samples result from pooled sequencing.
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
805 Model pooled samples using discrete genotypes across pools.
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
806 When using this flag, set --ploidy to the number of
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
807 alleles in each sample or use the --cnv-map to define
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
808 per-sample ploidy.
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
809 --pooled-continuous Output all alleles which pass input filters, regardles of
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
810 genotyping outcome or model.
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
811
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
812 **Reference allele**::
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
813
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
814 --use-reference-allele This flag includes the reference allele in the analysis as
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
815 if it is another sample from the same population.
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
816 --reference-quality MQ,BQ Assign mapping quality of MQ to the reference allele at each
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
817 site and base quality of BQ. default: 100,60
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
818
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
819 **Allele scope**::
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
820
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
821 --use-best-n-alleles N Evaluate only the best N SNP alleles, ranked by sum of
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
822 supporting quality scores. (Set to 0 to use all; default: all)
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
823 --max-complex-gap
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
824 --haplotype-length N Allow haplotype calls with contiguous embedded matches of up
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
825 to this length. Set N=-1 to disable clumping. (default: 3)
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
826 --min-repeat-size When assembling observations across repeats, require the total repeat
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
827 length at least this many bp. (default: 5)
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
828 --min-repeat-entropy N To detect interrupted repeats, build across sequence until it has
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
829 entropy > N bits per bp. Set to 0 to turn off. (default: 1)
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
830 --no-partial-observations Exclude observations which do not fully span the dynamically-determined
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
831 detection window. (default, use all observations, dividing partial
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
832 support across matching haplotypes when generating haplotypes.)
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
833
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
834 **Indel realignment**::
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
835
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
836 --dont-left-align-indels Turn off left-alignment of indels, which is enabled by default.
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
837
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
838 **Input filters**::
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
839
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
840 --use-duplicate-reads Include duplicate-marked alignments in the analysis.
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
841 default: exclude duplicates marked as such in alignments
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
842 --min-mapping-quality Q Exclude alignments from analysis if they have a mapping
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
843 quality less than Q. default: 1
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
844 --min-base-quality Q Exclude alleles from analysis if their supporting base
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
845 quality is less than Q. default: 0
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
846 --min-supporting-allele-qsum Q Consider any allele in which the sum of qualities of supporting
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
847 observations is at least Q. default: 0
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
848 --min-supporting-mapping-qsum Q Consider any allele in which and the sum of mapping qualities of
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
849 supporting reads is at least Q. default: 0
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
850 --mismatch-base-quality-threshold Q Count mismatches toward --read-mismatch-limit if the base
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
851 quality of the mismatch is >= Q. default: 10
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
852 --read-mismatch-limit N Exclude reads with more than N mismatches where each mismatch
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
853 has base quality >= mismatch-base-quality-threshold.
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
854 default: ~unbounded
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
855 --read-max-mismatch-fraction N Exclude reads with more than N [0,1] fraction of mismatches where
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
856 each mismatch has base quality >= mismatch-base-quality-threshold
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
857 default: 1.0
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
858 --read-snp-limit N Exclude reads with more than N base mismatches, ignoring gaps
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
859 with quality >= mismatch-base-quality-threshold.
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
860 default: ~unbounded
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
861 --read-indel-limit N Exclude reads with more than N separate gaps.
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
862 default: ~unbounded
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
863 --standard-filters Use stringent input base and mapping quality filters
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
864 Equivalent to -m 30 -q 20 -R 0 -S 0
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
865 --min-alternate-fraction N Require at least this fraction of observations supporting
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
866 an alternate allele within a single individual in the
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
867 in order to evaluate the position. default: 0.05
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
868 --min-alternate-count N Require at least this count of observations supporting
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
869 an alternate allele within a single individual in order
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
870 to evaluate the position. default: 2
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
871 --min-alternate-qsum N Require at least this sum of quality of observations supporting
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
872 an alternate allele within a single individual in order
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
873 to evaluate the position. default: 0
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
874 --min-alternate-total N Require at least this count of observations supporting
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
875 an alternate allele within the total population in order
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
876 to use the allele in analysis. default: 1
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
877 --min-coverage N Require at least this coverage to process a site. default: 0
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
878 --limit-coverage N Downsample per-sample coverage to this level if greater than this coverage.
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
879 default: no limit
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
880 --skip-coverage N Skip processing of alignments overlapping positions with coverage >N.
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
881 This filters sites above this coverage, but will also reduce data nearby.
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
882 default: no limit
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
883
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
884 **Population priors**::
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
885
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
886 --no-population-priors Equivalent to --pooled-discrete --hwe-priors-off and removal of
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
887 Ewens Sampling Formula component of priors.
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
888
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
889 **Mappability priors**::
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
890
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
891 --hwe-priors-off Disable estimation of the probability of the combination
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
892 arising under HWE given the allele frequency as estimated
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
893 by observation frequency.
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
894 --binomial-obs-priors-off Disable incorporation of prior expectations about observations.
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
895 Uses read placement probability, strand balance probability,
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
896 and read position (5'-3') probability.
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
897 --allele-balance-priors-off Disable use of aggregate probability of observation balance between alleles
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
898 as a component of the priors.
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
899
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
900 **Genotype likelihoods**::
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
901
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
902 --observation-bias FILE Read length-dependent allele observation biases from FILE.
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
903 The format is [length] [alignment efficiency relative to reference]
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
904 where the efficiency is 1 if there is no relative observation bias.
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
905 --base-quality-cap Q Limit estimated observation quality by capping base quality at Q.
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
906 --prob-contamination F An estimate of contamination to use for all samples. default: 10e-9
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
907 --legacy-gls Use legacy (polybayes equivalent) genotype likelihood calculations
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
908 --contamination-estimates FILE A file containing per-sample estimates of contamination, such as
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
909 those generated by VerifyBamID. The format should be:
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
910 sample p(read=R|genotype=AR) p(read=A|genotype=AA)
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
911 Sample '*' can be used to set default contamination estimates.
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
912
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
913 **Algorithmic features**::
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
914
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
915 --report-genotype-likelihood-max Report genotypes using the maximum-likelihood estimate provided
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
916 from genotype likelihoods.
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
917 --genotyping-max-iterations N Iterate no more than N times during genotyping step. default: 1000.
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
918 --genotyping-max-banddepth N Integrate no deeper than the Nth best genotype by likelihood when
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
919 genotyping. default: 6.
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
920 --posterior-integration-limits N,M Integrate all genotype combinations in our posterior space
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
921 which include no more than N samples with their Mth best
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
922 data likelihood. default: 1,3.
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
923 --exclude-unobserved-genotypes Skip sample genotypings for which the sample has no supporting reads.
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
924 --genotype-variant-threshold N Limit posterior integration to samples where the second-best
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
925 genotype likelihood is no more than log(N) from the highest
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
926 genotype likelihood for the sample. default: ~unbounded
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
927 --use-mapping-quality Use mapping quality of alleles when calculating data likelihoods.
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
928 --harmonic-indel-quality Use a weighted sum of base qualities around an indel, scaled by the
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
929 distance from the indel. By default use a minimum BQ in flanking sequence.
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
930 --read-dependence-factor N Incorporate non-independence of reads by scaling successive
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
931 observations by this factor during data likelihood
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
932 calculations. default: 0.9
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
933 --genotype-qualities Calculate the marginal probability of genotypes and report as GQ in
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
934 each sample field in the VCF output.
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
935
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
936 ------
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
937
25
bf27106652f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 24
diff changeset
938 **Acknowledgments**
13
2dd40b601766 Uploaded
devteam
parents:
diff changeset
939
2dd40b601766 Uploaded
devteam
parents:
diff changeset
940 The initial version of the wrapper was produced by Dan Blankenberg and upgraded by Anton Nekrutenko.
28
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941 TNG was developed by Bjoern Gruening.
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942 ]]>
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943 </help>
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944 <expand macro="citations">
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945 <citation type="bibtex">
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946 @article{Tange2011a,
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947 title = {GNU Parallel - The Command-Line Power Tool},
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948 author = {O. Tange},
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949 address = {Frederiksberg, Denmark},
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950 journal = {;login: The USENIX Magazine},
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951 month = {Feb},
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952 number = {1},
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953 volume = {36},
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954 url = {http://www.gnu.org/s/parallel},
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955 year = {2011},
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956 pages = {42-47}
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957 }
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958 </citation>
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959 </expand>
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960 </tool>