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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 84c34980b4fd8454c1cc630be5d6a3c22a4a1ef3"
author iuc
date Sat, 07 May 2022 19:49:37 +0000
parents a7c9782130e8
children
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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="20211222">parallel</requirement>
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12 </expand>
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13 <expand macro="version_command" />
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14 <command detect_errors="exit_code"><![CDATA[
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15 ##set up input files
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16
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17 #set $reference_fasta_filename = "localref.fa"
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18
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19 #if str( $reference_source.reference_source_selector ) == "history":
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20 ln -s -f '${reference_source.ref_file}' '${reference_fasta_filename}' &&
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21 samtools faidx '${reference_fasta_filename}' 2>&1 || echo "Error running samtools faidx for FreeBayes" >&2 &&
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22 #else:
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23 #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path )
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24 #end if
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26 #if $reference_source.batchmode.processmode == 'merge':
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27 #set $input_bamfiles = $reference_source.batchmode.input_bams
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28 #else:
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29 #set $input_bamfiles = [ $reference_source.batchmode.input_bams ]
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30 #end if
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32 #for $bam_count, $input_bam in enumerate( $input_bamfiles ):
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33 #if $input_bam.ext == 'bam':
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34 ln -s -f '${input_bam}' 'b_${bam_count}.bam' &&
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35 ln -s -f '${input_bam.metadata.bam_index}' 'b_${bam_count}.bam.bai' &&
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36 #elif $input_bam.ext == 'cram':
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37 ln -s -f '${input_bam}' 'b_${bam_count}.cram' &&
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38 ln -s -f '${input_bam.metadata.cram_index}' 'b_${bam_count}.cram.crai' &&
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39 #end if
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40 #end for
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42 ## Tabixize optional input_variant_vcf file (for --variant-input option)
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43 #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( $options_type.optional_inputs.input_variant_type.input_variant_type_selector ) == "provide_vcf":
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44 ln -s -f '${options_type.optional_inputs.input_variant_type.input_variant_vcf}' input_variant_vcf.vcf.gz &&
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45 ln -s -f '${Tabixized_input}' input_variant_vcf.vcf.gz.tbi &&
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46 #end if
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47
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48 ##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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49 #if str( $target_limit_type.target_limit_type_selector ) == "limit_by_target_file":
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50 ln -s '${target_limit_type.input_target_bed}' regions_all.bed &&
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51 #elif str( $target_limit_type.target_limit_type_selector ) == "limit_by_region":
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52 printf '${target_limit_type.region_chromosome}\t${target_limit_type.region_start}\t${target_limit_type.region_end}' > regions_all.bed &&
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53 #else
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54 ##divide up the regions in the bam file for efficient processing
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55 #for $bam_count, $input_bam in enumerate( $input_bamfiles ):
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56 samtools view -H b_${bam_count}.${input_bam.ext}|
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57 grep '^@SQ' |
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58 cut -f 2- |
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59 awk '{ gsub("^SN:","",$1); gsub("^LN:","",$2); print $1"\t0\t"$2; }' >> regions_all.bed &&
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60 #end for
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61 #end if
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62
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63 sort -u regions_all.bed > regions_uniq.bed &&
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64 ## split into even small chunks, this has some disatvantages and will not be used for the moment
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65 ## bedtools makewindows -b regions_uniq.bed -w 10000000 -s 9990000 > regions.bed &&
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66
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67 mkdir vcf_output failed_alleles trace &&
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69 ## Finished setting up inputs
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71 for i in `cat regions_uniq.bed | awk '{print $1":"$2".."$3}'`;
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72 do
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73 echo "
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75 ## COMMAND LINE STARTS HERE
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77 freebayes
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79 --region '\$i'
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80
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81 #for $bam_count, $input_bam in enumerate( $input_bamfiles ):
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82 --bam 'b_${bam_count}.${input_bam.ext}'
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83 #end for
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84 --fasta-reference '${reference_fasta_filename}'
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86 ## Outputs
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87 --vcf './vcf_output/part_\$i.vcf'
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88
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89 ## Coverage
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90 #if str($coverage_options.coverage_options_selector) == "set":
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91 @COVERAGE@
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92 #end if
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93
25
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94 ##advanced options
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95 #if str( $options_type.options_type_selector ) == "simple":
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96 #pass
25
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97 #elif str( $options_type.options_type_selector ) == "simple_w_filters":
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98 --standard-filters
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99 #elif str( $options_type.options_type_selector ) == "naive":
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100 --haplotype-length 0
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101 --min-alternate-count 1
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102 --min-alternate-fraction 0.05
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103 --pooled-continuous
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104 --report-monomorphic
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105 #elif str( $options_type.options_type_selector ) == "naive_w_filters":
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106 --haplotype-length 0
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107 --min-alternate-count 1
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108 --min-alternate-fraction 0.05
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109 --pooled-continuous
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110 --report-monomorphic
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111 --standard-filters
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112 #elif str( $options_type.options_type_selector ) == "full":
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113 #if str( $options_type.optional_inputs.optional_inputs_selector ) == 'set':
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114 ${options_type.optional_inputs.report_monomorphic}
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115
25
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116 #if $options_type.optional_inputs.output_trace_option:
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117 --trace ./trace/part_'\$i'.txt
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118 #end if
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119 #if $options_type.optional_inputs.output_failed_alleles_option:
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120 --failed-alleles ./failed_alleles/part_'\$i'.bed
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121 #end if
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122 #if $options_type.optional_inputs.samples:
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123 --samples '${options_type.optional_inputs.samples}'
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124 #end if
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125 #if $options_type.optional_inputs.populations:
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126 --populations '${options_type.optional_inputs.populations}'
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127 #end if
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128 #if $options_type.optional_inputs.A:
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129 --cnv-map '${options_type.optional_inputs.A}'
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130 #end if
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131 #if str( $options_type.optional_inputs.input_variant_type.input_variant_type_selector ) == "provide_vcf":
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132 --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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133 ${options_type.optional_inputs.input_variant_type.only_use_input_alleles}
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134 #end if
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135 #if $options_type.optional_inputs.haplotype_basis_alleles:
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136 --haplotype-basis-alleles '${options_type.optional_inputs.haplotype_basis_alleles}'
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137 #end if
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138 #if $options_type.optional_inputs.observation_bias:
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139 --observation-bias '${options_type.optional_inputs.observation_bias}'
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140 #end if
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141 #if $options_type.optional_inputs.contamination_estimates:
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142 --contamination-estimates '${options_type.optional_inputs.contamination_estimates}'
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143 #end if
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144 $options_type.optional_inputs.trim_complex_tail
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145 #end if
23
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146
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147 ## REPORTING
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148 #if str( $options_type.reporting.reporting_selector ) == "set":
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149 --pvar ${options_type.reporting.pvar}
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150 #end if
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151 ## POPULATION MODEL
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152 #if str( $options_type.population_model.population_model_selector ) == "set":
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153 --theta ${options_type.population_model.T}
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154 --ploidy ${options_type.population_model.P}
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155 ${options_type.population_model.J}
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156 ${options_type.population_model.K}
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157 #end if
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158
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159 ## REFERENCE ALLELE
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160 #if str( $options_type.reference_allele.reference_allele_selector ) == "set":
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161 ${options_type.reference_allele.Z}
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162 --reference-quality '${options_type.reference_allele.reference_quality}'
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163 #end if
13
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164
25
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165 ## ALLELE SCOPE
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166 #if str( $options_type.allele_scope.allele_scope_selector ) == "set":
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167 ${options_type.allele_scope.I}
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168 ${options_type.allele_scope.i}
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169 ${options_type.allele_scope.X}
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170 ${options_type.allele_scope.u}
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171 ${options_type.allele_scope.no_partial_observations}
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172
28
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173 -n ${options_type.allele_scope.n}
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174
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175 --haplotype-length ${options_type.allele_scope.haplotype_length}
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176 --min-repeat-size ${options_type.allele_scope.min_repeat_length}
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177 --min-repeat-entropy ${options_type.allele_scope.min_repeat_entropy}
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178 #end if
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179
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180 ## REALIGNMENT
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181 ${options_type.O}
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182
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183 ##INPUT FILTERS
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184 #if str( $options_type.input_filters.input_filters_selector ) == "set":
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185 ${options_type.input_filters.standard_filters}
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186 ${options_type.input_filters.use_duplicate_reads}
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187 --min-mapping-quality ${options_type.input_filters.min_mapping_quality}
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188 --min-base-quality ${options_type.input_filters.min_base_quality}
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189 --min-supporting-allele-qsum ${options_type.input_filters.min_supporting_allele_qsum}
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190 --min-supporting-mapping-qsum ${options_type.input_filters.min_supporting_mapping_qsum}
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191 #if str( $options_type.input_filters.mismatch_filters.mismatch_filters_selector ) == "set":
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192 --mismatch-base-quality-threshold ${options_type.input_filters.mismatch_filters.mismatch_base_quality_threshold}
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193 #if str($options_type.input_filters.mismatch_filters.read_mismatch_limit)
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194 --read-mismatch-limit ${options_type.input_filters.mismatch_filters.read_mismatch_limit}
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195 #end if
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196 --read-max-mismatch-fraction ${options_type.input_filters.mismatch_filters.read_max_mismatch_fraction}
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197 --read-snp-limit ${options_type.input_filters.mismatch_filters.read_snp_limit}
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198 #end if
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199 --read-indel-limit ${options_type.input_filters.read_indel_limit}
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200 --min-alternate-fraction ${options_type.input_filters.min_alternate_fraction}
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201 --min-alternate-qsum ${options_type.input_filters.min_alternate_qsum}
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202 --min-alternate-count ${options_type.input_filters.min_alternate_count}
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203 --min-alternate-total ${options_type.input_filters.min_alternate_total}
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204 #end if
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205
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206 ## POPULATION AND MAPPABILITY PRIORS
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207 #if str( $options_type.population_mappability_priors.population_mappability_priors_selector ) == "set":
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208 ${options_type.population_mappability_priors.k}
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209 ${options_type.population_mappability_priors.w}
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210 ${options_type.population_mappability_priors.V}
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211 ${options_type.population_mappability_priors.a}
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212 #end if
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213
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214 ## GENOTYPE LIKELIHOODS
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215 #if str( $options_type.genotype_likelihoods.genotype_likelihoods_selector ) == "set":
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216 ${$options_type.genotype_likelihoods.experimental_gls}
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217
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218 --base-quality-cap ${$options_type.genotype_likelihoods.base_quality_cap}
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219 --prob-contamination ${$options_type.genotype_likelihoods.prob_contamination}
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220 #end if
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221
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222 ## ALGORITHMIC FEATURES
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223 #if str( $options_type.algorithmic_features.algorithmic_features_selector ) == "set":
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224 -B '${options_type.algorithmic_features.B}'
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225 -W '${options_type.algorithmic_features.W}'
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226 -D '${options_type.algorithmic_features.D}'
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227
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228 #if str($options_type.algorithmic_features.genotype_variant_threshold)
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229 -S ${options_type.algorithmic_features.genotype_variant_threshold}
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230 #end if
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231
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232 ${options_type.algorithmic_features.N}
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233 ${options_type.algorithmic_features.j}
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234 ${options_type.algorithmic_features.H}
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235 ${options_type.algorithmic_features.genotype_qualities}
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236 ${options_type.algorithmic_features.report_genotype_likelihood_max}
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237
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238 --genotyping-max-banddepth ${options_type.algorithmic_features.genotyping_max_banddepth}
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239 #end if
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240 #end if
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241
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242 ";
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243 done > freebayes_commands.sh &&
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244
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245 cat freebayes_commands.sh |
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246 parallel --will-cite -j \${GALAXY_SLOTS:-1} &&
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247
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248 ## make VCF header
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249 grep "^#" "./vcf_output/part_\$i.vcf" > header.txt &&
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250
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251 for i in `cat regions_uniq.bed | awk '{print $1":"$2".."$3}'`;
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252 do
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253 ## if this fails then it bails out the script
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254 cat "./vcf_output/part_\$i.vcf" | grep -v "^#" || true
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255 ;
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256 done | sort -k1,1 -k2,2n -k5,5 -u | cat header.txt - > '${output_vcf}'
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257
23
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258 #if str( $options_type.options_type_selector ) == "full":
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259 #if str( $options_type.optional_inputs.optional_inputs_selector ) == 'set':
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260 #if $options_type.optional_inputs.output_failed_alleles_option:
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261 &&
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262 for i in `cat regions.bed | awk '{print $1":"$2".."$3}'`;
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263 do
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264 cat "./failed_alleles/part_\$i.bed"
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265 ;
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266 done > '${output_failed_alleles_bed}'
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267 #end if
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268
23
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269 #if $options_type.optional_inputs.output_trace_option:
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270 &&
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271 for i in `cat regions.bed | awk '{print $1":"$2".."$3}'`;
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272 do
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273 cat './trace/part_\$i.txt'
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274 ;
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275 done > '${output_trace}'
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276 #end if
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277 #end if
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278 #end if
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279 ]]></command>
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280
23
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281 <inputs>
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282 <conditional name="reference_source">
25
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283 <param name="reference_source_selector" type="select" label="Choose the source for the reference genome">
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284 <option value="cached">Locally cached</option>
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285 <option value="history">History</option>
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286 </param>
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287 <when value="cached">
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288 <expand macro="input_bam">
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289 <expand macro="validation" />
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290 </expand>
23
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291 <param name="ref_file" type="select" label="Using reference genome">
27
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292 <options from_data_table="fasta_indexes" />
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293 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input dataset"/>
23
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294 </param>
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295 </when>
23
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296 <when value="history"> <!-- FIX ME!!!! -->
27
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297 <expand macro="input_bam" />
23
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298 <param name="ref_file" type="data" format="fasta" label="Use the following dataset as the reference sequence"
25
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299 help="You can upload a FASTA sequence to the history and use it as reference" />
23
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300 </when>
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301 </conditional>
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302 <conditional name="target_limit_type">
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303 <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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304 <option value="do_not_limit" selected="true">Do not limit</option>
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305 <option value="limit_by_target_file">Limit by target file</option>
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306 <option value="limit_by_region">Limit to region</option>
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307 </param>
28
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308 <when value="do_not_limit" />
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309 <when value="limit_by_target_file">
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310 <param name="input_target_bed" argument="--targets" type="data" format="bed" label="Limit analysis to regions in this BED dataset" />
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311 </when>
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312 <when value="limit_by_region">
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313 <param name="region_chromosome" argument="--region" type="text" label="Region Chromosome" value="" /> <!--only once? -->
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314 <param name="region_start" type="integer" label="Region Start" value="" />
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315 <param name="region_end" type="integer" label="Region End" value="" />
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316 </when>
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317 </conditional>
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318 <conditional name="coverage_options">
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319 <param name="coverage_options_selector" type="select" label="Read coverage"
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320 help="Sets --min-coverage, --limit-coverage, and --skip-coverage">
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321 <option value="do_not_set" selected="true">Use defaults</option>
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322 <option value="set">Specify coverage options</option>
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323 </param>
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324 <when value="set">
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325 <expand macro="par_min_cov" />
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326 </when>
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327 <when value="do_not_set" />
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328 </conditional>
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329 <conditional name="options_type">
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330 <param name="options_type_selector" type="select" label="Choose parameter selection level"
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331 help="Select how much control over the freebayes run you need">
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332 <option value="simple" selected="true">1. Simple diploid calling</option>
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333 <option value="simple_w_filters">2. Simple diploid calling with filtering and coverage</option>
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334 <option value="naive">3. Frequency-based pooled calling</option>
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335 <option value="naive_w_filters">4. Frequency-based pooled calling with filtering and coverage</option>
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336 <option value="full">5. Full list of options</option>
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337 </param>
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338 <when value="full">
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339
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340 <conditional name="optional_inputs">
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341 <param name="optional_inputs_selector" type="select" label="Additional inputs"
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342 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">
23
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343 <option value="do_not_set" selected="true">Do not provide additional inputs</option>
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344 <option value="set">Provide additional inputs</option>
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345 </param>
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346 <when value="set">
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347 <param name="output_failed_alleles_option" argument="--failed-alleles" type="boolean" truevalue="--failed-alleles" falsevalue="" checked="false"
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348 label="Write out failed alleles file" />
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349 <param name="output_trace_option" argument="--trace" type="boolean" truevalue="--trace" falsevalue="" checked="false"
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350 label="Write out algorithm trace file" />
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351 <param argument="--samples" type="data" format="txt"
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352 label="Limit analysis to samples listed (one per line) in this dataset" optional="true"
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353 help="By default FreeBayes will analyze all samples in its input BAM datasets" />
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354 <param argument="--populations" type="data" format="txt" optional="true"
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355 label="Populations dataset"
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356 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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357 <param name="A" argument="--cnv-map" type="data" format="bed" optional="true"
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358 label="Read a copy number map from a BED dataset"
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359 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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360 <conditional name="input_variant_type">
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361 <param name="input_variant_type_selector" type="select" label="Provide variants dataset">
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362 <option value="do_not_provide" selected="true">Do not provide</option>
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363 <option value="provide_vcf">Provide VCF dataset</option>
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364 </param>
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365 <when value="do_not_provide" />
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366 <when value="provide_vcf">
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367 <param name="input_variant_vcf" argument="--variant-input" type="data" format="vcf_bgzip"
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368 label="Use variants reported in this VCF dataset as input to the algorithm">
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369 <conversion name="Tabixized_input" type="tabix" />
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370 </param>
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371 <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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372 label="Only provide variant calls and genotype likelihoods for sites in VCF" />
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373 </when>
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374 </conditional>
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375 <param name="haplotype_basis_alleles" argument="--haplotype-basis-alleles" type="data" format="vcf" optional="true"
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376 label="Only use variant alleles provided in this input VCF for the construction of complex or haplotype alleles" />
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377 <param name="report_monomorphic" argument="--report-monomorphic" type="boolean" truevalue="--report-monomorphic" falsevalue="" checked="false"
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378 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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379 <param name="observation_bias" argument="--observation-bias" type="data" format="tabular" optional="true"
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380 label="Load read length-dependent allele observation biases from"
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381 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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382 <param name="contamination_estimates" argument="--contamination-estimates" type="data" format="tabular" optional="true"
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383 label="Upload per-sample estimates of contamination from"
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384 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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385 <param name="trim_complex_tail" argument="--trim-complex-tail" type="boolean" truevalue="--trim-complex-tail" falsevalue=""
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386 label="Trim trailing reference matches" />
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387 </when>
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388 <when value="do_not_set" />
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389 </conditional>
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390
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391 <!-- reporting -->
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392 <conditional name="reporting">
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393 <param name="reporting_selector" type="select" label="Reporting options" help="Sets -P --pvar option">
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394 <option value="do_not_set" selected="true">Use defaults</option>
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395 <option value="set">Set reporting options</option>
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396 </param>
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397 <when value="set">
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398 <param argument="--pvar" type="float" value="0.0"
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399 label="Report sites if the probability that there is a polymorphism at the site is greater than"
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400 help="Note that post-filtering is generally recommended over the use of this parameter" />
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401 </when>
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402 <when value="do_not_set" />
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403 </conditional>
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404
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405 <!-- population model -->
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406 <conditional name="population_model">
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407 <param name="population_model_selector" type="select" label="Population model options"
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408 help="Sets --theta, --ploidy, --pooled-discrete, and --pooled-continuous options">
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409 <option value="do_not_set" selected="true">Use defaults</option>
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410 <option value="set">Set population model options</option>
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411 </param>
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412 <when value="set">
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413 <param name="T" argument="--theta" type="float" value="0.001"
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414 label="The expected mutation rate or pairwise nucleotide diversity among the population under analysis"
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415 help="This serves as the single parameter to the Ewens Sampling Formula prior model" />
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416 <param name="P" argument="--ploidy" type="integer" value="2"
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417 label="Set ploidy for the analysis" />
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418 <param name="J" argument="--pooled-discrete" type="boolean" truevalue="-J" falsevalue="" checked="false"
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419 label="Assume that samples result from pooled sequencing"
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420 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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421 <param name="K" argument="--poled-continuous" type="boolean" truevalue="-K" falsevalue="" checked="false"
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422 label="Output all alleles which pass input filters, regardles of genotyping outcome or model" />
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423 </when>
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424 <when value="do_not_set" />
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425 </conditional>
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426
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diff changeset
427 <!-- reference allele -->
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428 <conditional name="reference_allele">
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429 <param name="reference_allele_selector" type="select" label="Reference allele options"
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430 help="Sets --use-reference-allele and --reference-quality options">
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431 <option value="do_not_set" selected="true">Use defaults</option>
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432 <option value="set">Set reference allele options</option>
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433 </param>
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434 <when value="set">
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435 <param name="Z" argument="--use-reference-allele" type="boolean" truevalue="-Z" falsevalue="" checked="false"
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436 label="Include the reference allele in the analysis as if it is another sample from the same population" />
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437 <param name="reference_quality" argument="--reference-quality" type="text" value="100,60"
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438 label="Assign mapping quality of MQ (100) to the reference allele at each site and base quality of BQ (60)" />
23
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439 </when>
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440 <when value="do_not_set" />
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441 </conditional>
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442
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443 <!-- allelic scope -->
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444 <conditional name="allele_scope">
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445 <param name="allele_scope_selector" type="select" label="Allelic scope options"
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446 help="Sets -I, i, -X, -u, -n, --haplotype-length, --min-repeat-size, --min-repeat-entropy, and --no-partial-observations options">
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447 <option value="do_not_set" selected="true">Use defaults</option>
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448 <option value="set">Set alleic scope options</option>
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449 </param>
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450 <when value="set">
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451 <param name="I" argument="--no-snps" type="boolean" truevalue="-I" falsevalue="" checked="false"
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452 label="Ignore SNP alleles" />
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453 <param name="i" argument="--no-indels" type="boolean" truevalue="-i" falsevalue="" checked="false"
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454 label="Ignore indels alleles" />
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parents: 27
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455 <param name="X" argument="--no-mnps" type="boolean" truevalue="-X" falsevalue="" checked="false"
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parents: 27
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456 label="Ignore multi-nucleotide polymorphisms, MNPs" />
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457 <param name="u" argument="--no-complex" type="boolean" truevalue="-u" falsevalue="" checked="false"
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458 label="Ignore complex events (composites of other classes)" />
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459 <param name="n" argument="--use-best-n-alleles" type="integer" value="0"
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460 label="How many best SNP alleles to evaluate"
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461 help="Alleles are ranked by the sum of supporting quality scores. Set to 0 to evaluate all" />
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462 <param name="haplotype_length" argument="--haplotype-length" type="integer" value="3"
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463 label="Allow haplotype calls with contiguous embedded matches of up to (nucleotides)" />
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parents: 27
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464 <param name="min_repeat_length" argument="--min-repeat-size" type="integer" value="5"
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465 label="When assembling observations across repeats, require the total repeat length at least this many bp" />
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466 <param name="min_repeat_entropy" argument="--min-repeat-entropy" type="integer" value="1"
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467 label="To detect interrupted repeats, build across sequence until it has entropy > (bits per bp)" />
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468 <param name="no_partial_observations" argument="--no-partial-observations" type="boolean" truevalue="--no-partial-observations" falsevalue="" checked="false"
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469 label="Exclude observations which do not fully span the dynamically-determined detection window"
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470 help="By default, FreeBayes uses all observations, dividing partial support across matching haplotypes when generating haplotypes" />
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471 </when>
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472 <when value="do_not_set" />
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473 </conditional>
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474
23
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diff changeset
475 <!-- indel realignment -->
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476 <param name="O" argument="--dont-left-align-indels" type="boolean" truevalue="-O" falsevalue="" checked="false"
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diff changeset
477 label="Turn off left-alignment of indels" />
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parents: 24
diff changeset
478
23
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parents: 22
diff changeset
479 <!-- input filters -->
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480 <conditional name="input_filters">
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481 <param name="input_filters_selector" type="select" label="Input filters">
23
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diff changeset
482 <option value="do_not_set" selected="true">No input filters (default)</option>
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483 <option value="set">Set input filters</option>
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diff changeset
484 </param>
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485 <when value="set">
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486 <param argument="--standard-filters" type="boolean" truevalue="--standard-filters" falsevalue="" checked="false"
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487 label="Use stringent input base and mapping quality filters"
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488 help="--min-mapping-quality 30 --min-base-quality 20, --min-supporting-allele-qsum 0 --genotype-variant-threshold 0"/>
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489 <param argument="--use-duplicate-reads" type="boolean" truevalue="--use-duplicate-reads" falsevalue="" checked="false"
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490 label="Include duplicate-marked alignments in the analysis" />
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491 <param argument="--min-mapping-quality" type="integer" value="1"
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492 label="Exclude alignments from analysis if they have a mapping quality less than" />
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493 <param argument="--min-base-quality" type="integer" value="0"
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diff changeset
494 label="Exclude alleles from analysis if their supporting base quality less than" />
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495 <param argument="--min-supporting-allele-qsum" type="integer" value="0"
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496 label="Consider any allele in which the sum of qualities of supporting observations is at least" />
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497 <param argument="--min-supporting-mapping-qsum" type="integer" value="0"
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diff changeset
498 label="Consider any allele in which and the sum of mapping qualities of supporting reads is at least" />
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diff changeset
499 <conditional name="mismatch_filters">
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500 <param name="mismatch_filters_selector" type="select" label="Mismatch filters"
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parents: 24
diff changeset
501 help="Sets -Q, -U, -z, and &#36; options">
23
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diff changeset
502 <option value="do_not_set" selected="true">No mismatch filters (default)</option>
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503 <option value="set">Set mismatch filters</option>
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diff changeset
504 </param>
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505 <when value="set">
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parents: 30
diff changeset
506 <param argument="--mismatch-base-quality-threshold" type="integer" value="10"
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diff changeset
507 label="Count mismatches toward -U (option below) if the base quality of the mismatch is >=" />
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diff changeset
508 <param argument="--read-mismatch-limit" type="integer" value="1000" optional="true"
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diff changeset
509 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
510 help="default=~unbounded" />
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diff changeset
511 <param argument="--read-max-mismatch-fraction" type="float" value="1.0" min="0.0" max="1.0"
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diff changeset
512 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
513 <param name="read_snp_limit" argument="--read-snp-limit" type="integer" value="1000"
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diff changeset
514 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
515 help="default=~unbounded" />
23
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diff changeset
516 </when>
28
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parents: 27
diff changeset
517 <when value="do_not_set" />
23
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diff changeset
518 </conditional>
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parents: 30
diff changeset
519 <param argument="--read-indel-limit" type="integer" value="1000"
28
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parents: 27
diff changeset
520 label="Exclude reads with more than this number of separate gaps"
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parents: 27
diff changeset
521 help="default=~unbounded" />
31
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parents: 30
diff changeset
522 <param argument="--min-alternate-fraction" type="float" value="0.05"
28
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parents: 27
diff changeset
523 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
524 <param argument="--min-alternate-qsum" type="integer" value="0"
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parents: 30
diff changeset
525 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
526 <param argument="--min-alternate-count" type="integer" value="2"
28
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parents: 27
diff changeset
527 label="Require at least this count of observations supporting an alternate allele within a single individual in order to evaluate the position" />
31
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iuc
parents: 30
diff changeset
528 <param argument="--min-alternate-total" type="integer" value="1"
28
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parents: 27
diff changeset
529 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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diff changeset
530 </when>
28
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parents: 27
diff changeset
531 <when value="do_not_set" />
23
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parents: 22
diff changeset
532 </conditional>
25
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parents: 24
diff changeset
533
23
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parents: 22
diff changeset
534 <!-- population and mappability priors -->
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parents: 22
diff changeset
535 <conditional name="population_mappability_priors">
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diff changeset
536 <param name="population_mappability_priors_selector" type="select" label="Population and mappability priors"
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diff changeset
537 help="Sets -k, -w, -V, and -a options">
23
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diff changeset
538 <option value="do_not_set" selected="true">Use defaults</option>
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parents: 22
diff changeset
539 <option value="set">Set population and mappability priors</option>
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diff changeset
540 </param>
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diff changeset
541 <when value="set">
28
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parents: 27
diff changeset
542 <param name="k" argument="--no-population-priors" type="boolean" truevalue="-k" falsevalue="" checked="false"
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diff changeset
543 label="No population priors"
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parents: 27
diff changeset
544 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
545 <param name="w" argument="--hwe-priors-off" type="boolean" truevalue="-w" falsevalue="" checked="false"
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parents: 27
diff changeset
546 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
547 <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
548 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
549 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
550 <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
iuc
parents: 27
diff changeset
551 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
552 </when>
28
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parents: 27
diff changeset
553 <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
554 </conditional>
25
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parents: 24
diff changeset
555
23
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parents: 22
diff changeset
556 <!-- 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 <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
558 <param name="genotype_likelihoods_selector" type="select" label="Genotype likelihood options"
28
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parents: 27
diff changeset
559 help="Sets --base-quality-cap, --experimental-gls, and --prob-contamination options">
23
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parents: 22
diff changeset
560 <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
561 <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
562 </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
563 <when value="set">
28
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parents: 27
diff changeset
564 <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
565 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
566 <param name="experimental_gls" argument="--experimental-gls" type="boolean" truevalue="--experimental-gls" falsevalue="" checked="false"
25
bf27106652f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 24
diff changeset
567 label="Generate genotype likelihoods using 'effective base depth' metric qual = 1-BaseQual * 1-MapQual"
28
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iuc
parents: 27
diff changeset
568 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
569 <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
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parents: 27
diff changeset
570 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
571 </when>
28
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parents: 27
diff changeset
572 <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
573 </conditional>
25
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parents: 24
diff changeset
574
23
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parents: 22
diff changeset
575 <!-- algorithmic features -->
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parents: 22
diff changeset
576 <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
577 <param name="algorithmic_features_selector" type="select" label="Algorithmic features"
25
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parents: 24
diff changeset
578 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
579 <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
580 <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
581 </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
582 <when value="set">
28
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parents: 27
diff changeset
583 <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
584 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
585 <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
586 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
587 <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
588 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
iuc
parents: 27
diff changeset
589 <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
590 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
591 <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
iuc
parents: 27
diff changeset
592 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
593 <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
594 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
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parents: 27
diff changeset
595 help="default=~unbounded" />
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596 <param name="j" argument="--use-mapping-quality" type="boolean" truevalue="-j" falsevalue="" checked="false"
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diff changeset
597 label="Use mapping quality of alleles when calculating data likelihoods" />
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598 <param name="H" argument="--harmonic-indel-quality" type="boolean" truevalue="-H" falsevalue="" checked="false"
25
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diff changeset
599 label="Use a weighted sum of base qualities around an indel, scaled by the distance from the indel"
28
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diff changeset
600 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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diff changeset
601 <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
602 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
iuc
parents: 27
diff changeset
603 <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
604 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
605 </when>
28
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parents: 27
diff changeset
606 <when value="do_not_set" />
23
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diff changeset
607 </conditional>
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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diff changeset
608 </when>
28
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diff changeset
609 <when value="simple" />
30
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diff changeset
610 <when value="simple_w_filters" />
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diff changeset
611 <when value="naive" />
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
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diff changeset
612 <when value="naive_w_filters" />
23
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 22
diff changeset
613 </conditional>
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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diff changeset
614 </inputs>
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 22
diff changeset
615 <outputs>
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 22
diff changeset
616 <data format="vcf" name="output_vcf" label="${tool.name} on ${on_string} (variants)" />
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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diff changeset
617 <data format="bed" name="output_failed_alleles_bed" label="${tool.name} on ${on_string} (failed alleles)">
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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parents: 22
diff changeset
618 <filter>( options_type['options_type_selector'] == 'cline' or options_type['options_type_selector'] == 'full' ) and options_type['optional_inputs']['optional_inputs_selector'] == 'set' and options_type['optional_inputs']['output_failed_alleles_option'] is True</filter>
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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parents: 22
diff changeset
619 </data>
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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parents: 22
diff changeset
620 <data format="txt" name="output_trace" label="${tool.name} on ${on_string} (trace)">
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 22
diff changeset
621 <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
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parents: 22
diff changeset
622 </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
623 </outputs>
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 22
diff changeset
624 <tests>
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 22
diff changeset
625 <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
626 <param name="reference_source_selector" value="history" />
27
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iuc
parents: 26
diff changeset
627 <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
628 <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
629 <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
630 <param name="options_type_selector" value="simple"/>
29
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parents: 28
diff changeset
631 <output name="output_vcf" file="freebayes-phix174-test1.vcf" lines_diff="4" />
23
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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 <test>
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 22
diff changeset
634 <param name="reference_source_selector" value="history" />
27
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iuc
parents: 26
diff changeset
635 <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
636 <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
637 <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
638 <param name="options_type_selector" value="naive_w_filters"/>
30
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iuc
parents: 29
diff changeset
639 <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
640 <param name="min_coverage" value="14"/>
29
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iuc
parents: 28
diff changeset
641 <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
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 <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
644 <param name="reference_source_selector" value="history" />
27
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iuc
parents: 26
diff changeset
645 <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
646 <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
647 <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
648 <param name="options_type_selector" value="naive_w_filters"/>
30
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iuc
parents: 29
diff changeset
649 <param name="coverage_options_selector" value="set" />
23
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devteam
parents: 22
diff changeset
650 <param name="min_coverage" value="14"/>
29
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parents: 28
diff changeset
651 <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
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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 <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
654 <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
655 <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
656 <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
657 <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
658 <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
659 <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
660 <param name="P" value="1"/>
32
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iuc
parents: 31
diff changeset
661 <param name="trim_complex_tail" value="--trim-complex-tail"/>
29
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parents: 28
diff changeset
662 <output name="output_vcf" file="freebayes-phix174-test4.vcf" lines_diff="4" />
23
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diff changeset
663 </test>
30
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664 <test>
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
665 <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
666 <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
667 <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
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diff changeset
668 <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
669 <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
670 <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
671 <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
672 <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
673 </test>
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
674 <test>
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="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
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676 <param name="processmode" value="individual" />
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677 <param name="ref_file" ftype="fasta" value="freebayes-hxb2.fasta"/>
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678 <param name="input_bams" ftype="bam" value="freebayes-hxb2.bam"/>
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679 <param name="options_type_selector" value="simple"/>
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680 <param name="coverage_options_selector" value="set" />
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681 <param name="limit_coverage" value="400" />
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682 <output name="output_vcf" file="freebayes-hxb2-test6.vcf" lines_diff="4" />
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683 </test>
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684 <test>
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685 <param name="reference_source_selector" value="history" />
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686 <param name="processmode" value="individual" />
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687 <param name="ref_file" ftype="fasta" value="freebayes-hxb2.fasta"/>
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688 <param name="input_bams" ftype="bam" value="freebayes-hxb2.bam"/>
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689 <param name="options_type_selector" value="simple"/>
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690 <param name="coverage_options_selector" value="set" />
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691 <param name="skip_coverage" value="100" />
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692 <output name="output_vcf" file="freebayes-hxb2-test7.vcf" lines_diff="4" />
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693 </test>
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694 <test> <!-- Test with CRAM -->
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695 <param name="reference_source_selector" value="history" />
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696 <param name="processmode" value="individual" />
8a7a42541080 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit cce7fcdd5e8ba8636c751f9f974bf07a6845ba1c"
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697 <param name="ref_file" ftype="fasta" value="freebayes-phix174.fasta"/>
8a7a42541080 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit cce7fcdd5e8ba8636c751f9f974bf07a6845ba1c"
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698 <param name="input_bams" ftype="cram" value="freebayes-phix174.cram"/>
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699 <param name="options_type_selector" value="simple"/>
34
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700 <output name="output_vcf" file="freebayes-phix174-test1.vcf" lines_diff="6" />
32
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701 </test>
23
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702 </tests>
30
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703 <help><![CDATA[
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704 **What it does**
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705
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706 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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707
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708 See https://github.com/ekg/freebayes for details on FreeBayes.
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709
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710 ------
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711
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712 **Description**
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713
28
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714 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.
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715
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716 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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717
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718 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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719
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720 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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721
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722 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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723
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724 -------
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725
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726 **Galaxy-specific options**
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727
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728 Galaxy allows five levels of control over FreeBayes options, provided by the **Choose parameter selection level** menu option. These are:
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729
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730 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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731 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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732 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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733 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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734 5. *Complete list of all options*: Gives you full control by exposing all FreeBayes options as Galaxy parameters.
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735
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736 ------
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737
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738 **Command-line parameters**
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739
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740 **Input**::
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741
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742 --bam FILE The file or set of BAM files to be analyzed.
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743 --bam-list FILE A file containing a list of BAM files to be analyzed.
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744
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745 --stdin Read BAM input on stdin.
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746 --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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747 An index file (FILE.fai) will be created if none exists.
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748 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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749 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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750 --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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751 --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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752 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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753 Either '-' or '..' maybe used as a separator.
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754 --samples FILE Limit analysis to samples listed (one per line) in the FILE.
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
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755 By default FreeBayes will analyze all samples in its input
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756 BAM files.
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757 --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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758 it is part of. The population-based bayesian inference model
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759 will then be partitioned on the basis of the populations.
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
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760 --cnv-map FILE Read a copy number map from the BED file FILE, which has
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
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761 either a sample-level ploidy:
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762 sample_name copy_number
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763 or a region-specific format:
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
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764 seq_name start end sample_name copy_number
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765 ... for each region in each sample which does not have the
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766 default copy number as set by --ploidy. These fields can be delimited
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767 by space or tab.
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768
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769 **Output**::
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770
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771 --vcf FILE Output VCF-format results to FILE. (default: stdout)
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diff changeset
772 --gvcf Write gVCF output, which indicates coverage in uncalled regions.
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
773 --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
774 --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
775 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
776 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
777 --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
778 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
779 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
780 --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
781 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
782 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
783 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
784 --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
785 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
786 alleles.
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
787 --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
788 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
789 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
790 --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
791 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
792 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
793 --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
794 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
795 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
796 --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
797
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
798 **Population model**::
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
799
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
800 --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
801 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
802 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
803 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
804 --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
805 --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
806 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
807 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
808 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
809 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
810 --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
811 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
812
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
813 **Reference allele**::
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
814
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
815 --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
816 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
817 --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
818 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
819
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
820 **Allele scope**::
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
821
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
822 --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
823 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
824 --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
825 --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
826 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
827 --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
828 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
829 --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
830 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
831 --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
832 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
833 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
834
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
835 **Indel realignment**::
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
836
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
837 --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
838
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
839 **Input filters**::
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
840
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
841 --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
842 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
843 --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
844 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
845 --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
846 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
847 --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
848 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
849 --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
850 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
851 --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
852 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
853 --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
854 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
855 default: ~unbounded
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
856 --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
857 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
858 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
859 --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
860 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
861 default: ~unbounded
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
862 --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
863 default: ~unbounded
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
864 --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
865 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
866 --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
867 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
868 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
869 --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
870 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
871 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
872 --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
873 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
874 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
875 --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
876 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
877 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
878 --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
879 --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
880 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
881 --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
882 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
883 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
884
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
885 **Population priors**::
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
886
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
887 --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
888 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
889
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
890 **Mappability priors**::
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
891
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
892 --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
893 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
894 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
895 --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
896 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
897 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
898 --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
899 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
900
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
901 **Genotype likelihoods**::
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
902
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
903 --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
904 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
905 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
906 --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
907 --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
908 --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
909 --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
910 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
911 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
912 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
913
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
914 **Algorithmic features**::
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
915
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
916 --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
917 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
918 --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
919 --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
920 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
921 --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
922 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
923 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
924 --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
925 --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
926 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
927 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
928 --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
929 --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
930 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
931 --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
932 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
933 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
934 --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
935 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
936
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
937 ------
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
938
25
bf27106652f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 24
diff changeset
939 **Acknowledgments**
13
2dd40b601766 Uploaded
devteam
parents:
diff changeset
940
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941 The initial version of the wrapper was produced by Dan Blankenberg and upgraded by Anton Nekrutenko.
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942 TNG was developed by Bjoern Gruening.
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943 ]]>
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944 </help>
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945 <expand macro="citations">
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946 <citation type="bibtex">
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947 @article{Tange2011a,
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948 title = {GNU Parallel - The Command-Line Power Tool},
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949 author = {O. Tange},
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950 address = {Frederiksberg, Denmark},
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951 journal = {;login: The USENIX Magazine},
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952 month = {Feb},
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953 number = {1},
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954 volume = {36},
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955 url = {http://www.gnu.org/s/parallel},
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956 year = {2011},
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957 pages = {42-47}
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958 }
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959 </citation>
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960 </expand>
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961 </tool>