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annotate freebayes.xml @ 40:0d8581534009 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 48700fed491e8056cddd1ee7d8bc9ca08e19fe8d
author iuc
date Tue, 05 Aug 2025 13:47:58 +0000
parents 85dc96ebc770
children
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0d8581534009 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 48700fed491e8056cddd1ee7d8bc9ca08e19fe8d
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1 <tool id="freebayes" name="FreeBayes" version="@TOOL_VERSION@+galaxy1" profile="23.0">
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2 <description>bayesian genetic variant detector</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <xrefs>
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7 <xref type="bio.tools">freebayes</xref>
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8 </xrefs>
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9 <expand macro="requirements">
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10 <requirement type="package" version="3.11">grep</requirement>
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11 <requirement type="package" version="5.3.1">gawk</requirement>
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12 <requirement type="package" version="20250622">parallel</requirement>
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13 </expand>
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14 <expand macro="version_command" />
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15 <command detect_errors="exit_code"><![CDATA[
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16 ##set up input files
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17
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18 #set $reference_fasta_filename = "localref.fa"
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19
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20 #if str( $reference_source.reference_source_selector ) == "history":
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21 ln -s -f '${reference_source.ref_file}' '${reference_fasta_filename}' &&
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22 samtools faidx '${reference_fasta_filename}' 2>&1 || echo "Error running samtools faidx for FreeBayes" >&2 &&
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23 #else:
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24 #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path )
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25 #end if
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27 #if $reference_source.batchmode.processmode == 'merge':
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28 #set $input_bamfiles = $reference_source.batchmode.input_bams
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29 #else:
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30 #set $input_bamfiles = [ $reference_source.batchmode.input_bams ]
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31 #end if
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33 #for $bam_count, $input_bam in enumerate( $input_bamfiles ):
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34 #if $input_bam.ext == 'bam':
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35 ln -s -f '${input_bam}' 'b_${bam_count}.bam' &&
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36 ln -s -f '${input_bam.metadata.bam_index}' 'b_${bam_count}.bam.bai' &&
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37 #elif $input_bam.ext == 'cram':
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38 ln -s -f '${input_bam}' 'b_${bam_count}.cram' &&
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39 ln -s -f '${input_bam.metadata.cram_index}' 'b_${bam_count}.cram.crai' &&
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40 #end if
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41 #end for
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43 ## For --variant-input option, create symlinks to vcf.bgzip input and its accompanying tabix index
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44 #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( $options_type.optional_inputs.input_variant_type.input_variant_type_selector ) == "provide_vcf":
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45 ln -s -f '${options_type.optional_inputs.input_variant_type.input_variant_vcf}' input_variant_vcf.vcf.gz &&
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46 ln -s '$options_type.optional_inputs.input_variant_type.input_variant_vcf.metadata.tabix_index' input_variant_vcf.vcf.gz.tbi &&
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47 #end if
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48
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49 ##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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50 #if str( $target_limit_type.target_limit_type_selector ) == "limit_by_target_file":
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51 ln -s '${target_limit_type.input_target_bed}' regions_all.bed &&
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52 #elif str( $target_limit_type.target_limit_type_selector ) == "limit_by_region":
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53 printf '${target_limit_type.region_chromosome}\t${target_limit_type.region_start}\t${target_limit_type.region_end}' > regions_all.bed &&
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54 #else
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55 ##divide up the regions in the bam file for efficient processing
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56 #for $bam_count, $input_bam in enumerate( $input_bamfiles ):
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57 samtools view -H b_${bam_count}.${input_bam.ext}|
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58 grep '^@SQ' |
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59 cut -f 2- |
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60 awk '{ gsub("^SN:","",$1); gsub("^LN:","",$2); print $1"\t0\t"$2; }' >> regions_all.bed &&
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61 #end for
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62 #end if
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63
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64 sort -u regions_all.bed > regions_uniq.bed &&
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65 ## split into even small chunks, this has some disatvantages and will not be used for the moment
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66 ## bedtools makewindows -b regions_uniq.bed -w 10000000 -s 9990000 > regions.bed &&
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67
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68 mkdir vcf_output failed_alleles trace &&
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70 ## Finished setting up inputs
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72 for i in `cat regions_uniq.bed | awk '{print $1":"$2".."$3}'`;
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73 do
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74 echo "
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76 ## COMMAND LINE STARTS HERE
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78 freebayes
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80 --region '\$i'
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81
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82 #for $bam_count, $input_bam in enumerate( $input_bamfiles ):
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83 --bam 'b_${bam_count}.${input_bam.ext}'
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84 #end for
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85 --fasta-reference '${reference_fasta_filename}'
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86
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87 ## Outputs
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88 --vcf './vcf_output/part_\$i.vcf'
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89
30
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90 ## Coverage
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91 #if str($coverage_options.coverage_options_selector) == "set":
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92 @COVERAGE@
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93 #end if
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94
25
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95 ##advanced options
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96 #if str( $options_type.options_type_selector ) == "simple":
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97 #pass
25
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98 #elif str( $options_type.options_type_selector ) == "simple_w_filters":
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99 --standard-filters
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100 #elif str( $options_type.options_type_selector ) == "naive":
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101 --haplotype-length 0
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102 --min-alternate-count 1
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103 --min-alternate-fraction 0.05
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104 --pooled-continuous
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105 --report-monomorphic
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106 #elif str( $options_type.options_type_selector ) == "naive_w_filters":
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107 --haplotype-length 0
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108 --min-alternate-count 1
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109 --min-alternate-fraction 0.05
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110 --pooled-continuous
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111 --report-monomorphic
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112 --standard-filters
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113 #elif str( $options_type.options_type_selector ) == "full":
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114 #if str( $options_type.optional_inputs.optional_inputs_selector ) == 'set':
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115 ${options_type.optional_inputs.report_monomorphic}
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116
25
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117 #if $options_type.optional_inputs.output_trace_option:
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118 --trace ./trace/part_'\$i'.txt
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119 #end if
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120 #if $options_type.optional_inputs.output_failed_alleles_option:
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121 --failed-alleles ./failed_alleles/part_'\$i'.bed
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122 #end if
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123 #if $options_type.optional_inputs.samples:
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124 --samples '${options_type.optional_inputs.samples}'
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125 #end if
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126 #if $options_type.optional_inputs.populations:
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127 --populations '${options_type.optional_inputs.populations}'
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128 #end if
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129 #if $options_type.optional_inputs.A:
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130 --cnv-map '${options_type.optional_inputs.A}'
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131 #end if
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132 #if str( $options_type.optional_inputs.input_variant_type.input_variant_type_selector ) == "provide_vcf":
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133 --variant-input 'input_variant_vcf.vcf.gz'
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134 ${options_type.optional_inputs.input_variant_type.only_use_input_alleles}
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135 #end if
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136 #if $options_type.optional_inputs.haplotype_basis_alleles:
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137 --haplotype-basis-alleles '${options_type.optional_inputs.haplotype_basis_alleles}'
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138 #end if
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139 #if $options_type.optional_inputs.observation_bias:
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140 --observation-bias '${options_type.optional_inputs.observation_bias}'
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141 #end if
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142 #if $options_type.optional_inputs.contamination_estimates:
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143 --contamination-estimates '${options_type.optional_inputs.contamination_estimates}'
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144 #end if
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145 $options_type.optional_inputs.trim_complex_tail
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146 #end if
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147
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148 ## REPORTING
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149 #if str( $options_type.reporting.reporting_selector ) == "set":
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150 --pvar ${options_type.reporting.pvar}
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151 #end if
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152 ## POPULATION MODEL
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153 #if str( $options_type.population_model.population_model_selector ) == "set":
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154 --theta ${options_type.population_model.T}
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155 --ploidy ${options_type.population_model.P}
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156 ${options_type.population_model.J}
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157 ${options_type.population_model.K}
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158 #end if
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159
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160 ## REFERENCE ALLELE
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161 #if str( $options_type.reference_allele.reference_allele_selector ) == "set":
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162 ${options_type.reference_allele.Z}
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163 --reference-quality '${options_type.reference_allele.reference_quality}'
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164 #end if
13
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165
25
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166 ## ALLELE SCOPE
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167 #if str( $options_type.allele_scope.allele_scope_selector ) == "set":
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168 ${options_type.allele_scope.I}
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169 ${options_type.allele_scope.i}
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170 ${options_type.allele_scope.X}
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171 ${options_type.allele_scope.u}
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172 ${options_type.allele_scope.no_partial_observations}
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173
28
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174 -n ${options_type.allele_scope.n}
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175
28
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176 --haplotype-length ${options_type.allele_scope.haplotype_length}
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177 --min-repeat-size ${options_type.allele_scope.min_repeat_length}
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178 --min-repeat-entropy ${options_type.allele_scope.min_repeat_entropy}
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179 #end if
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180
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181 ## REALIGNMENT
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182 ${options_type.O}
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183
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184 ##INPUT FILTERS
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185 #if str( $options_type.input_filters.input_filters_selector ) == "set":
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186 ${options_type.input_filters.standard_filters}
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187 ${options_type.input_filters.use_duplicate_reads}
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188 --min-mapping-quality ${options_type.input_filters.min_mapping_quality}
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189 --min-base-quality ${options_type.input_filters.min_base_quality}
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190 --min-supporting-allele-qsum ${options_type.input_filters.min_supporting_allele_qsum}
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191 --min-supporting-mapping-qsum ${options_type.input_filters.min_supporting_mapping_qsum}
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192 #if str( $options_type.input_filters.mismatch_filters.mismatch_filters_selector ) == "set":
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193 --mismatch-base-quality-threshold ${options_type.input_filters.mismatch_filters.mismatch_base_quality_threshold}
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194 #if str($options_type.input_filters.mismatch_filters.read_mismatch_limit)
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195 --read-mismatch-limit ${options_type.input_filters.mismatch_filters.read_mismatch_limit}
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196 #end if
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197 --read-max-mismatch-fraction ${options_type.input_filters.mismatch_filters.read_max_mismatch_fraction}
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198 --read-snp-limit ${options_type.input_filters.mismatch_filters.read_snp_limit}
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199 #end if
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200 --read-indel-limit ${options_type.input_filters.read_indel_limit}
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201 --min-alternate-fraction ${options_type.input_filters.min_alternate_fraction}
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202 --min-alternate-qsum ${options_type.input_filters.min_alternate_qsum}
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203 --min-alternate-count ${options_type.input_filters.min_alternate_count}
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204 --min-alternate-total ${options_type.input_filters.min_alternate_total}
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205 #end if
25
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206
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207 ## POPULATION AND MAPPABILITY PRIORS
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208 #if str( $options_type.population_mappability_priors.population_mappability_priors_selector ) == "set":
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209 ${options_type.population_mappability_priors.k}
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210 ${options_type.population_mappability_priors.w}
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211 ${options_type.population_mappability_priors.V}
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212 ${options_type.population_mappability_priors.a}
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213 #end if
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214
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215 ## GENOTYPE LIKELIHOODS
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216 #if str( $options_type.genotype_likelihoods.genotype_likelihoods_selector ) == "set":
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217 ${$options_type.genotype_likelihoods.experimental_gls}
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218
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219 --base-quality-cap ${$options_type.genotype_likelihoods.base_quality_cap}
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220 --prob-contamination ${$options_type.genotype_likelihoods.prob_contamination}
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221 #end if
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222
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223 ## ALGORITHMIC FEATURES
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224 #if str( $options_type.algorithmic_features.algorithmic_features_selector ) == "set":
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225 -B '${options_type.algorithmic_features.B}'
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226 -W '${options_type.algorithmic_features.W}'
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227 -D '${options_type.algorithmic_features.D}'
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228
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229 #if str($options_type.algorithmic_features.genotype_variant_threshold)
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230 -S ${options_type.algorithmic_features.genotype_variant_threshold}
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231 #end if
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232
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233 ${options_type.algorithmic_features.N}
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234 ${options_type.algorithmic_features.j}
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235 ${options_type.algorithmic_features.H}
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236 ${options_type.algorithmic_features.genotype_qualities}
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237 ${options_type.algorithmic_features.report_genotype_likelihood_max}
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238
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239 --genotyping-max-banddepth ${options_type.algorithmic_features.genotyping_max_banddepth}
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240 #end if
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241 #end if
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242
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243 #if str($output_options.flavor) == "gvcf":
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244 --gvcf
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245 #elif str($output_options.flavor) == "gvcf_custom":
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246 --gvcf
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247 #if $output_options.gvcf_block_size == 0:
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248 ## special-casing the 0 case for performance
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249 --gvcf-dont-use-chunk t
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250 #else:
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251 --gvcf-chunk $output_options.gvcf_block_size
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252 #end if
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253 #end if
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254
25
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255 ";
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256 done > freebayes_commands.sh &&
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257
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258 cat freebayes_commands.sh |
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259 parallel --will-cite -j \${GALAXY_SLOTS:-1} &&
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260
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261 ## make VCF header
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262 grep "^#" "./vcf_output/part_\$i.vcf" > header.txt &&
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263
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264 for i in `cat regions_uniq.bed | awk '{print $1":"$2".."$3}'`;
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265 do
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266 ## if this fails then it bails out the script
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267 cat "./vcf_output/part_\$i.vcf" | grep -v "^#" || true
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268 ;
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269 done | sort -k1,1 -k2,2n -k5,5 -u | cat header.txt - > '${output_vcf}'
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270
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271 #if str( $options_type.options_type_selector ) == "full":
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272 #if str( $options_type.optional_inputs.optional_inputs_selector ) == 'set':
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273 #if $options_type.optional_inputs.output_failed_alleles_option:
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274 &&
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275 for i in `cat regions.bed | awk '{print $1":"$2".."$3}'`;
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276 do
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277 cat "./failed_alleles/part_\$i.bed"
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278 ;
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279 done > '${output_failed_alleles_bed}'
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280 #end if
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281
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282 #if $options_type.optional_inputs.output_trace_option:
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283 &&
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284 for i in `cat regions.bed | awk '{print $1":"$2".."$3}'`;
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285 do
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286 cat './trace/part_\$i.txt'
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287 ;
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288 done > '${output_trace}'
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289 #end if
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290 #end if
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291 #end if
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292 ]]></command>
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293
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294 <inputs>
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295 <conditional name="reference_source">
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296 <param name="reference_source_selector" type="select" label="Choose the source for the reference genome">
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297 <option value="cached">Locally cached</option>
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298 <option value="history">History</option>
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299 </param>
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300 <when value="cached">
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301 <expand macro="input_bam">
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302 <expand macro="validation" />
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303 </expand>
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304 <param name="ref_file" type="select" label="Using reference genome">
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305 <options from_data_table="fasta_indexes" />
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306 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input dataset"/>
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307 </param>
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308 </when>
23
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309 <when value="history"> <!-- FIX ME!!!! -->
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310 <expand macro="input_bam" />
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311 <param name="ref_file" type="data" format="fasta" label="Use the following dataset as the reference sequence"
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312 help="You can upload a FASTA sequence to the history and use it as reference" />
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313 </when>
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314 </conditional>
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315 <conditional name="target_limit_type">
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316 <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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317 <option value="do_not_limit" selected="true">Do not limit</option>
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318 <option value="limit_by_target_file">Limit by target file</option>
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319 <option value="limit_by_region">Limit to region</option>
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320 </param>
28
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321 <when value="do_not_limit" />
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322 <when value="limit_by_target_file">
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323 <param name="input_target_bed" argument="--targets" type="data" format="bed" label="Limit analysis to regions in this BED dataset" />
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324 </when>
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325 <when value="limit_by_region">
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326 <param name="region_chromosome" argument="--region" type="text" label="Region Chromosome" value="" /> <!--only once? -->
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327 <param name="region_start" type="integer" label="Region Start" value="" />
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328 <param name="region_end" type="integer" label="Region End" value="" />
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329 </when>
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330 </conditional>
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331 <conditional name="coverage_options">
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332 <param name="coverage_options_selector" type="select" label="Read coverage"
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333 help="Sets --min-coverage, --limit-coverage, and --skip-coverage">
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334 <option value="do_not_set" selected="true">Use defaults</option>
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335 <option value="set">Specify coverage options</option>
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336 </param>
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337 <when value="set">
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338 <expand macro="par_min_cov" />
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339 </when>
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340 <when value="do_not_set" />
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341 </conditional>
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342 <conditional name="options_type">
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343 <param name="options_type_selector" type="select" label="Choose parameter selection level"
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344 help="Select how much control over the freebayes run you need">
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345 <option value="simple" selected="true">1. Simple diploid calling</option>
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346 <option value="simple_w_filters">2. Simple diploid calling with filtering and coverage</option>
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347 <option value="naive">3. Frequency-based pooled calling</option>
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348 <option value="naive_w_filters">4. Frequency-based pooled calling with filtering and coverage</option>
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349 <option value="full">5. Full list of options</option>
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350 </param>
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351 <when value="full">
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352
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353 <conditional name="optional_inputs">
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354 <param name="optional_inputs_selector" type="select" label="Additional inputs"
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355 help="Sets --samples, --populations, --cnv-map, --trace, --failed-alleles, --variant-input, --only-use-input-alleles, --haplotype-basis-alleles, --report-all-haplotype-alleles, --report-monomorphic options, --observation-bias, --contamination-estimates and --trim-complex-tail">
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356 <option value="do_not_set" selected="true">Do not provide additional inputs</option>
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357 <option value="set">Provide additional inputs</option>
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358 </param>
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359 <when value="set">
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360 <param name="output_failed_alleles_option" argument="--failed-alleles" type="boolean" truevalue="--failed-alleles" falsevalue="" checked="false"
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361 label="Write out failed alleles file" />
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362 <param name="output_trace_option" argument="--trace" type="boolean" truevalue="--trace" falsevalue="" checked="false"
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363 label="Write out algorithm trace file" />
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364 <param argument="--samples" type="data" format="txt"
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365 label="Limit analysis to samples listed (one per line) in this dataset" optional="true"
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366 help="By default FreeBayes will analyze all samples in its input BAM datasets" />
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367 <param argument="--populations" type="data" format="txt" optional="true"
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368 label="Populations dataset"
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369 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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370 <param name="A" argument="--cnv-map" type="data" format="bed" optional="true"
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371 label="Read a copy number map from a BED dataset"
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372 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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373 <conditional name="input_variant_type">
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374 <param name="input_variant_type_selector" type="select" label="Provide variants dataset">
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375 <option value="do_not_provide" selected="true">Do not provide</option>
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376 <option value="provide_vcf">Provide VCF dataset</option>
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377 </param>
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378 <when value="do_not_provide" />
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379 <when value="provide_vcf">
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380 <param name="input_variant_vcf" argument="--variant-input" type="data" format="vcf_bgzip"
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381 label="Use variants reported in this VCF dataset as input to the algorithm"/>
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382 <param argument="--only-use-input-alleles" type="boolean" truevalue="--only-use-input-alleles" falsevalue="" checked="false"
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383 label="Only provide variant calls and genotype likelihoods for sites in VCF" />
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384 </when>
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385 </conditional>
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386 <param argument="--haplotype-basis-alleles" type="data" format="vcf" optional="true"
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387 label="Only use variant alleles provided in this input VCF for the construction of complex or haplotype alleles" />
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388 <param argument="--report-monomorphic" type="boolean" truevalue="--report-monomorphic" falsevalue="" checked="false"
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389 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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390 <param argument="--observation-bias" type="data" format="tabular" optional="true"
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391 label="Load read length-dependent allele observation biases from"
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392 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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393 <param argument="--contamination-estimates" type="data" format="tabular" optional="true"
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394 label="Upload per-sample estimates of contamination from"
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395 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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396 <param argument="--trim-complex-tail" type="boolean" truevalue="--trim-complex-tail" falsevalue=""
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397 label="Trim trailing reference matches" />
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398 </when>
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399 <when value="do_not_set" />
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400 </conditional>
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401
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diff changeset
402 <!-- reporting -->
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403 <conditional name="reporting">
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404 <param name="reporting_selector" type="select" label="Reporting options" help="Sets -P --pvar option">
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405 <option value="do_not_set" selected="true">Use defaults</option>
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406 <option value="set">Set reporting options</option>
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407 </param>
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408 <when value="set">
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409 <param argument="--pvar" type="float" value="0.0"
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410 label="Report sites if the probability that there is a polymorphism at the site is greater than"
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411 help="Note that post-filtering is generally recommended over the use of this parameter" />
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412 </when>
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413 <when value="do_not_set" />
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414 </conditional>
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415
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416 <!-- population model -->
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417 <conditional name="population_model">
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418 <param name="population_model_selector" type="select" label="Population model options"
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419 help="Sets --theta, --ploidy, --pooled-discrete, and --pooled-continuous options">
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420 <option value="do_not_set" selected="true">Use defaults</option>
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421 <option value="set">Set population model options</option>
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422 </param>
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423 <when value="set">
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424 <param name="T" argument="--theta" type="float" value="0.001"
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425 label="The expected mutation rate or pairwise nucleotide diversity among the population under analysis"
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426 help="This serves as the single parameter to the Ewens Sampling Formula prior model" />
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427 <param name="P" argument="--ploidy" type="integer" value="2"
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428 label="Set ploidy for the analysis" />
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429 <param name="J" argument="--pooled-discrete" type="boolean" truevalue="-J" falsevalue="" checked="false"
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430 label="Assume that samples result from pooled sequencing"
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431 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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432 <param name="K" argument="--poled-continuous" type="boolean" truevalue="-K" falsevalue="" checked="false"
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433 label="Output all alleles which pass input filters, regardles of genotyping outcome or model" />
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434 </when>
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435 <when value="do_not_set" />
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436 </conditional>
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437
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438 <!-- reference allele -->
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439 <conditional name="reference_allele">
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440 <param name="reference_allele_selector" type="select" label="Reference allele options"
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441 help="Sets --use-reference-allele and --reference-quality options">
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442 <option value="do_not_set" selected="true">Use defaults</option>
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443 <option value="set">Set reference allele options</option>
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diff changeset
444 </param>
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445 <when value="set">
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446 <param name="Z" argument="--use-reference-allele" type="boolean" truevalue="-Z" falsevalue="" checked="false"
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447 label="Include the reference allele in the analysis as if it is another sample from the same population" />
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448 <param argument="--reference-quality" type="text" value="100,60"
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449 label="Assign mapping quality of MQ (100) to the reference allele at each site and base quality of BQ (60)" />
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450 </when>
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451 <when value="do_not_set" />
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452 </conditional>
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453
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454 <!-- allelic scope -->
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455 <conditional name="allele_scope">
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456 <param name="allele_scope_selector" type="select" label="Allelic scope options"
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457 help="Sets -I, i, -X, -u, -n, --haplotype-length, --min-repeat-size, --min-repeat-entropy, and --no-partial-observations options">
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458 <option value="do_not_set" selected="true">Use defaults</option>
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459 <option value="set">Set alleic scope options</option>
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460 </param>
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461 <when value="set">
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462 <param name="I" argument="--no-snps" type="boolean" truevalue="-I" falsevalue="" checked="false"
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diff changeset
463 label="Ignore SNP alleles" />
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464 <param name="i" argument="--no-indels" type="boolean" truevalue="-i" falsevalue="" checked="false"
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465 label="Ignore indels alleles" />
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466 <param name="X" argument="--no-mnps" type="boolean" truevalue="-X" falsevalue="" checked="false"
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parents: 27
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467 label="Ignore multi-nucleotide polymorphisms, MNPs" />
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468 <param name="u" argument="--no-complex" type="boolean" truevalue="-u" falsevalue="" checked="false"
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diff changeset
469 label="Ignore complex events (composites of other classes)" />
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470 <param name="n" argument="--use-best-n-alleles" type="integer" value="0"
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471 label="How many best SNP alleles to evaluate"
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472 help="Alleles are ranked by the sum of supporting quality scores. Set to 0 to evaluate all" />
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473 <param argument="--haplotype-length" type="integer" value="3"
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diff changeset
474 label="Allow haplotype calls with contiguous embedded matches of up to (nucleotides)" />
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475 <param name="min_repeat_length" argument="--min-repeat-size" type="integer" value="5"
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476 label="When assembling observations across repeats, require the total repeat length at least this many bp" />
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477 <param argument="--min-repeat-entropy" type="integer" value="1"
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diff changeset
478 label="To detect interrupted repeats, build across sequence until it has entropy > (bits per bp)" />
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parents: 39
diff changeset
479 <param argument="--no-partial-observations" type="boolean" truevalue="--no-partial-observations" falsevalue="" checked="false"
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parents: 24
diff changeset
480 label="Exclude observations which do not fully span the dynamically-determined detection window"
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diff changeset
481 help="By default, FreeBayes uses all observations, dividing partial support across matching haplotypes when generating haplotypes" />
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diff changeset
482 </when>
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diff changeset
483 <when value="do_not_set" />
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diff changeset
484 </conditional>
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diff changeset
485
23
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diff changeset
486 <!-- indel realignment -->
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diff changeset
487 <param name="O" argument="--dont-left-align-indels" type="boolean" truevalue="-O" falsevalue="" checked="false"
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diff changeset
488 label="Turn off left-alignment of indels" />
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diff changeset
489
23
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parents: 22
diff changeset
490 <!-- input filters -->
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diff changeset
491 <conditional name="input_filters">
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492 <param name="input_filters_selector" type="select" label="Input filters">
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diff changeset
493 <option value="do_not_set" selected="true">No input filters (default)</option>
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494 <option value="set">Set input filters</option>
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diff changeset
495 </param>
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496 <when value="set">
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497 <param argument="--standard-filters" type="boolean" truevalue="--standard-filters" falsevalue="" checked="false"
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498 label="Use stringent input base and mapping quality filters"
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diff changeset
499 help="--min-mapping-quality 30 --min-base-quality 20, --min-supporting-allele-qsum 0 --genotype-variant-threshold 0"/>
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500 <param argument="--use-duplicate-reads" type="boolean" truevalue="--use-duplicate-reads" falsevalue="" checked="false"
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501 label="Include duplicate-marked alignments in the analysis" />
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502 <param argument="--min-mapping-quality" type="integer" value="1"
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diff changeset
503 label="Exclude alignments from analysis if they have a mapping quality less than" />
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504 <param argument="--min-base-quality" type="integer" value="0"
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diff changeset
505 label="Exclude alleles from analysis if their supporting base quality less than" />
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diff changeset
506 <param argument="--min-supporting-allele-qsum" type="integer" value="0"
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diff changeset
507 label="Consider any allele in which the sum of qualities of supporting observations is at least" />
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parents: 30
diff changeset
508 <param argument="--min-supporting-mapping-qsum" type="integer" value="0"
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diff changeset
509 label="Consider any allele in which and the sum of mapping qualities of supporting reads is at least" />
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diff changeset
510 <conditional name="mismatch_filters">
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diff changeset
511 <param name="mismatch_filters_selector" type="select" label="Mismatch filters"
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parents: 24
diff changeset
512 help="Sets -Q, -U, -z, and &#36; options">
23
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diff changeset
513 <option value="do_not_set" selected="true">No mismatch filters (default)</option>
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diff changeset
514 <option value="set">Set mismatch filters</option>
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diff changeset
515 </param>
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diff changeset
516 <when value="set">
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diff changeset
517 <param argument="--mismatch-base-quality-threshold" type="integer" value="10"
28
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diff changeset
518 label="Count mismatches toward -U (option below) if the base quality of the mismatch is >=" />
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diff changeset
519 <param argument="--read-mismatch-limit" type="integer" value="1000" optional="true"
28
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diff changeset
520 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
521 help="default=~unbounded" />
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diff changeset
522 <param argument="--read-max-mismatch-fraction" type="float" value="1.0" min="0.0" max="1.0"
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parents: 27
diff changeset
523 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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parents: 39
diff changeset
524 <param argument="--read-snp-limit" type="integer" value="1000"
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parents: 27
diff changeset
525 label="Exclude reads with more than N base mismatches, ignoring gaps with quality >= mismatch-base-quality-threshold (third option above)"
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parents: 27
diff changeset
526 help="default=~unbounded" />
23
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parents: 22
diff changeset
527 </when>
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parents: 27
diff changeset
528 <when value="do_not_set" />
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parents: 22
diff changeset
529 </conditional>
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parents: 30
diff changeset
530 <param argument="--read-indel-limit" type="integer" value="1000"
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parents: 27
diff changeset
531 label="Exclude reads with more than this number of separate gaps"
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parents: 27
diff changeset
532 help="default=~unbounded" />
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parents: 30
diff changeset
533 <param argument="--min-alternate-fraction" type="float" value="0.05"
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parents: 27
diff changeset
534 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
535 <param argument="--min-alternate-qsum" type="integer" value="0"
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parents: 30
diff changeset
536 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
537 <param argument="--min-alternate-count" type="integer" value="2"
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parents: 27
diff changeset
538 label="Require at least this count of observations supporting an alternate allele within a single individual in order to evaluate the position" />
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parents: 30
diff changeset
539 <param argument="--min-alternate-total" type="integer" value="1"
28
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parents: 27
diff changeset
540 label="Require at least this count of observations supporting an alternate allele within the total population in order to use the allele in analysis" />
23
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parents: 22
diff changeset
541 </when>
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parents: 27
diff changeset
542 <when value="do_not_set" />
23
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parents: 22
diff changeset
543 </conditional>
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parents: 24
diff changeset
544
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parents: 22
diff changeset
545 <!-- population and mappability priors -->
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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parents: 22
diff changeset
546 <conditional name="population_mappability_priors">
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parents: 22
diff changeset
547 <param name="population_mappability_priors_selector" type="select" label="Population and mappability priors"
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parents: 27
diff changeset
548 help="Sets -k, -w, -V, and -a options">
23
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parents: 22
diff changeset
549 <option value="do_not_set" selected="true">Use defaults</option>
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parents: 22
diff changeset
550 <option value="set">Set population and mappability priors</option>
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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parents: 22
diff changeset
551 </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
552 <when value="set">
28
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iuc
parents: 27
diff changeset
553 <param name="k" argument="--no-population-priors" type="boolean" truevalue="-k" falsevalue="" checked="false"
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iuc
parents: 27
diff changeset
554 label="No population priors"
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parents: 27
diff changeset
555 help="Equivalent to --pooled-discrete --hwe-priors-off and removal of Ewens Sampling Formula component of priors" />
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iuc
parents: 27
diff changeset
556 <param name="w" argument="--hwe-priors-off" type="boolean" truevalue="-w" 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
557 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
558 <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
559 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
560 help="Uses read placement probability, strand balance probability, and read position (5&#39;'-3&#39;') probability" />
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parents: 27
diff changeset
561 <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
562 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
563 </when>
28
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parents: 27
diff changeset
564 <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
565 </conditional>
25
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parents: 24
diff changeset
566
23
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parents: 22
diff changeset
567 <!-- 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
568 <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
569 <param name="genotype_likelihoods_selector" type="select" label="Genotype likelihood options"
28
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parents: 27
diff changeset
570 help="Sets --base-quality-cap, --experimental-gls, and --prob-contamination options">
23
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parents: 22
diff changeset
571 <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
572 <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
573 </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
574 <when value="set">
40
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parents: 39
diff changeset
575 <param argument="--base-quality-cap" type="integer" value="0"
28
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parents: 27
diff changeset
576 label="Limit estimated observation quality by capping base quality at" />
40
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parents: 39
diff changeset
577 <param argument="--experimental-gls" type="boolean" truevalue="--experimental-gls" falsevalue="" checked="false"
25
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parents: 24
diff changeset
578 label="Generate genotype likelihoods using 'effective base depth' metric qual = 1-BaseQual * 1-MapQual"
28
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parents: 27
diff changeset
579 help="Incorporate partial observations. This is the default when contamination estimates are provided. Optimized for diploid samples" />
40
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parents: 39
diff changeset
580 <param argument="--prob-contamination" type="float" value="10e-9"
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parents: 27
diff changeset
581 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
582 </when>
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parents: 27
diff changeset
583 <when value="do_not_set" />
23
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parents: 22
diff changeset
584 </conditional>
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parents: 24
diff changeset
585
23
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parents: 22
diff changeset
586 <!-- algorithmic features -->
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parents: 22
diff changeset
587 <conditional name="algorithmic_features">
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parents: 22
diff changeset
588 <param name="algorithmic_features_selector" type="select" label="Algorithmic features"
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parents: 24
diff changeset
589 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
590 <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
591 <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
592 </param>
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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diff changeset
593 <when value="set">
40
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parents: 39
diff changeset
594 <param argument="--report-genotype-likelihood-max" type="boolean" truevalue="--report-genotype-likelihood-max" falsevalue="" checked="false"
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parents: 27
diff changeset
595 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
596 <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
iuc
parents: 27
diff changeset
597 label="Iterate no more than N times during genotyping step" />
40
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parents: 39
diff changeset
598 <param argument="--genotyping-max-banddepth" type="integer" value="6"
28
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599 label="Integrate no deeper than the Nth best genotype by likelihood when genotyping" />
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600 <param name="W" argument="--posterior-integration-limits" type="text" value="1,3"
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601 label="Integrate all genotype combinations in our posterior space which include no more than N (1) samples with their Mth (3) best data likelihood" />
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602 <param name="N" argument="--exclude-unobserved-genotypes" type="boolean" truevalue="--exclude-unobserved-genotypes" falsevalue="" checked="false"
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603 label="Skip sample genotypings for which the sample has no supporting reads" />
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604 <param argument="--genotype-variant-threshold" type="integer" value="" optional="true"
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605 label="Limit posterior integration to samples where the second-best genotype likelihood is no more than log(N) from the highest genotype likelihood for the sample"
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606 help="default=~unbounded" />
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607 <param name="j" argument="--use-mapping-quality" type="boolean" truevalue="-j" falsevalue="" checked="false"
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608 label="Use mapping quality of alleles when calculating data likelihoods" />
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609 <param name="H" argument="--harmonic-indel-quality" type="boolean" truevalue="-H" falsevalue="" checked="false"
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diff changeset
610 label="Use a weighted sum of base qualities around an indel, scaled by the distance from the indel"
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611 help="By default, FreeBayes uses a minimum Base Quality in flanking sequence" />
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612 <param name="D" argument="--read-dependence-factor" type="float" value="0.9"
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613 label="Incorporate non-independence of reads by scaling successive observations by this factor during data likelihood calculations" />
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614 <param argument="--genotype-qualities" type="boolean" truevalue="--genotype-qualities" falsevalue="" checked="false"
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615 label="Calculate the marginal probability of genotypes and report as GQ in each sample field in the VCF output" />
23
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616 </when>
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617 <when value="do_not_set" />
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618 </conditional>
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619 </when>
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620 <when value="simple" />
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621 <when value="simple_w_filters" />
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622 <when value="naive" />
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623 <when value="naive_w_filters" />
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624 </conditional>
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parents: 39
diff changeset
625 <conditional name="output_options">
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626 <param name="flavor" type="select" label="Type of main output to produce" help="The tool will, by default, produce VCF output with information about sites with called variants. If you want also information (such as depth of coverage) about non-called sites, you can use the gVCF or gVCF with custom block size options. The first collapses the stats of entire blocks of consecutive non-called sites into one non-call record. The second gives you control over how many consecutive non-called sites should be combined into a non-call record.">
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627 <option value="vcf">VCF (default)</option>
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628 <option value="gvcf">gVCF (--gvcf)</option>
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629 <option value="gvcf_custom">gVCF with custom block size</option>
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diff changeset
630 </param>
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parents: 39
diff changeset
631 <when value="vcf" />
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parents: 39
diff changeset
632 <when value="gvcf" />
0d8581534009 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 48700fed491e8056cddd1ee7d8bc9ca08e19fe8d
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parents: 39
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633 <when value="gvcf_custom">
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634 <param name="gvcf_block_size" type="integer" value="0" min="0" max="2147483647" label="Maximal block size for consecutive non-called sites" help="Consolidate data from any non-called site together with the N next non-called sites into one gVCF record, i.e. produce gVCF block records of maximally N+1 sites. Blocks can be shorter if terminated by the end of a chromosome or a site with a called variant. Setting this parameter to 0 produces a separate record for every non-called site, but can result in very large output." />
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635 </when>
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636 </conditional>
23
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diff changeset
637 </inputs>
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diff changeset
638 <outputs>
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639 <data format="vcf" name="output_vcf" label="${tool.name} on ${on_string} (variants)" />
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640 <data format="bed" name="output_failed_alleles_bed" label="${tool.name} on ${on_string} (failed alleles)">
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641 <filter>( options_type['options_type_selector'] == 'cline' or options_type['options_type_selector'] == 'full' ) and options_type['optional_inputs']['optional_inputs_selector'] == 'set' and options_type['optional_inputs']['output_failed_alleles_option'] is True</filter>
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642 </data>
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643 <data format="txt" name="output_trace" label="${tool.name} on ${on_string} (trace)">
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parents: 22
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644 <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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645 </data>
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diff changeset
646 </outputs>
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647 <tests>
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648 <test expect_num_outputs="1">
23
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649 <param name="reference_source_selector" value="history" />
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650 <param name="processmode" value="individual" />
23
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651 <param name="ref_file" ftype="fasta" value="freebayes-phix174.fasta"/>
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652 <param name="input_bams" ftype="bam" value="freebayes-phix174.bam"/>
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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653 <param name="options_type_selector" value="simple"/>
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654 <output name="output_vcf" file="freebayes-phix174-test1.vcf" lines_diff="4" />
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655 </test>
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656 <test expect_num_outputs="1">
0d8581534009 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 48700fed491e8056cddd1ee7d8bc9ca08e19fe8d
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657 <param name="reference_source_selector" value="history" />
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658 <param name="processmode" value="individual" />
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659 <param name="ref_file" ftype="fasta" value="freebayes-phix174.fasta" />
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diff changeset
660 <param name="input_bams" ftype="bam" value="freebayes-phix174.bam" />
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diff changeset
661 <param name="options_type_selector" value="simple" />
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662 <conditional name="output_options">
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663 <param name="flavor" value="gvcf" />
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664 </conditional>
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665 <output name="output_vcf" file="freebayes-phix174.gvcf" lines_diff="4" />
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666 </test>
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667 <test expect_num_outputs="1">
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668 <param name="reference_source_selector" value="history" />
0d8581534009 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 48700fed491e8056cddd1ee7d8bc9ca08e19fe8d
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669 <param name="processmode" value="individual" />
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670 <param name="ref_file" ftype="fasta" value="freebayes-phix174.fasta" />
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671 <param name="input_bams" ftype="bam" value="freebayes-phix174.bam" />
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672 <param name="options_type_selector" value="simple" />
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673 <conditional name="output_options">
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674 <param name="flavor" value="gvcf_custom" />
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675 </conditional>
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676 <!-- This test produces one record per reference position
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677 so the test file only contains the first part of the expected output up to the second variant site -->
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678 <output name="output_vcf" file="freebayes-phix174.full.sample.gvcf" compare="contains" lines_diff="2" />
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diff changeset
679 </test>
0d8581534009 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 48700fed491e8056cddd1ee7d8bc9ca08e19fe8d
iuc
parents: 39
diff changeset
680 <test expect_num_outputs="1">
23
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 22
diff changeset
681 <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
682 <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
683 <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
684 <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
685 <param name="options_type_selector" value="naive_w_filters"/>
30
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
686 <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
687 <param name="min_coverage" value="14"/>
29
156b60c1530f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 99e8a87a2993ae644df15756044a40a42aa7a05b
iuc
parents: 28
diff changeset
688 <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
devteam
parents: 22
diff changeset
689 </test>
38
e698621cca1f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit cdd582adf568e80558740ec7ff51c9447948cf77
iuc
parents: 37
diff changeset
690 <!-- Test that user-provided (variant-input option) sites are included in output -->
40
0d8581534009 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 48700fed491e8056cddd1ee7d8bc9ca08e19fe8d
iuc
parents: 39
diff changeset
691 <test expect_num_outputs="1">
23
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 22
diff changeset
692 <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
693 <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
694 <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
695 <param name="input_bams" ftype="bam" value="freebayes-phix174.bam"/>
38
e698621cca1f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit cdd582adf568e80558740ec7ff51c9447948cf77
iuc
parents: 37
diff changeset
696 <param name="options_type_selector" value="full"/>
e698621cca1f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit cdd582adf568e80558740ec7ff51c9447948cf77
iuc
parents: 37
diff changeset
697 <conditional name="optional_inputs">
e698621cca1f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit cdd582adf568e80558740ec7ff51c9447948cf77
iuc
parents: 37
diff changeset
698 <param name="optional_inputs_selector" value="set" />
e698621cca1f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit cdd582adf568e80558740ec7ff51c9447948cf77
iuc
parents: 37
diff changeset
699 <conditional name="input_variant_type">
e698621cca1f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit cdd582adf568e80558740ec7ff51c9447948cf77
iuc
parents: 37
diff changeset
700 <param name="input_variant_type_selector" value="provide_vcf" />
e698621cca1f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit cdd582adf568e80558740ec7ff51c9447948cf77
iuc
parents: 37
diff changeset
701 <param name="input_variant_vcf" value="freebayes-phix174-input-sites-test3.vcf.bgzip" />
e698621cca1f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit cdd582adf568e80558740ec7ff51c9447948cf77
iuc
parents: 37
diff changeset
702 </conditional>
e698621cca1f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit cdd582adf568e80558740ec7ff51c9447948cf77
iuc
parents: 37
diff changeset
703 </conditional>
e698621cca1f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit cdd582adf568e80558740ec7ff51c9447948cf77
iuc
parents: 37
diff changeset
704 <output name="output_vcf">
e698621cca1f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit cdd582adf568e80558740ec7ff51c9447948cf77
iuc
parents: 37
diff changeset
705 <assert_contents>
e698621cca1f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit cdd582adf568e80558740ec7ff51c9447948cf77
iuc
parents: 37
diff changeset
706 <has_line_matching expression="phiX174&#009;1134&#009;\.&#009;A&#009;\.&#009;.+"/>
e698621cca1f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit cdd582adf568e80558740ec7ff51c9447948cf77
iuc
parents: 37
diff changeset
707 </assert_contents>
e698621cca1f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit cdd582adf568e80558740ec7ff51c9447948cf77
iuc
parents: 37
diff changeset
708 </output>
23
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 22
diff changeset
709 </test>
40
0d8581534009 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 48700fed491e8056cddd1ee7d8bc9ca08e19fe8d
iuc
parents: 39
diff changeset
710 <test expect_num_outputs="1">
23
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 22
diff changeset
711 <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
712 <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
713 <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
714 <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
715 <param name="options_type_selector" value="full"/>
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 22
diff changeset
716 <param name="population_model_selector" value="set"/>
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 22
diff changeset
717 <param name="P" value="1"/>
32
8a7a42541080 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit cce7fcdd5e8ba8636c751f9f974bf07a6845ba1c"
iuc
parents: 31
diff changeset
718 <param name="trim_complex_tail" value="--trim-complex-tail"/>
29
156b60c1530f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 99e8a87a2993ae644df15756044a40a42aa7a05b
iuc
parents: 28
diff changeset
719 <output name="output_vcf" file="freebayes-phix174-test4.vcf" lines_diff="4" />
23
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 22
diff changeset
720 </test>
40
0d8581534009 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 48700fed491e8056cddd1ee7d8bc9ca08e19fe8d
iuc
parents: 39
diff changeset
721 <test expect_num_outputs="1">
30
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
722 <param name="reference_source_selector" value="history" />
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
723 <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
724 <param name="ref_file" ftype="fasta" value="freebayes-hxb2.fasta"/>
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
725 <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
726 <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
727 <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
728 <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
729 <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
parents: 29
diff changeset
730 </test>
40
0d8581534009 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 48700fed491e8056cddd1ee7d8bc9ca08e19fe8d
iuc
parents: 39
diff changeset
731 <test expect_num_outputs="1">
30
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
732 <param name="reference_source_selector" value="history" />
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
733 <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
734 <param name="ref_file" ftype="fasta" value="freebayes-hxb2.fasta"/>
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
735 <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
736 <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
737 <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
738 <param name="limit_coverage" value="400" />
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
739 <output name="output_vcf" file="freebayes-hxb2-test6.vcf" lines_diff="4" />
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
740 </test>
40
0d8581534009 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 48700fed491e8056cddd1ee7d8bc9ca08e19fe8d
iuc
parents: 39
diff changeset
741 <test expect_num_outputs="1">
30
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
742 <param name="reference_source_selector" value="history" />
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
743 <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
744 <param name="ref_file" ftype="fasta" value="freebayes-hxb2.fasta"/>
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
745 <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
746 <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
747 <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
748 <param name="skip_coverage" value="100" />
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
749 <output name="output_vcf" file="freebayes-hxb2-test7.vcf" lines_diff="4" />
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
750 </test>
40
0d8581534009 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 48700fed491e8056cddd1ee7d8bc9ca08e19fe8d
iuc
parents: 39
diff changeset
751 <test expect_num_outputs="1"> <!-- Test with CRAM -->
32
8a7a42541080 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit cce7fcdd5e8ba8636c751f9f974bf07a6845ba1c"
iuc
parents: 31
diff changeset
752 <param name="reference_source_selector" value="history" />
8a7a42541080 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit cce7fcdd5e8ba8636c751f9f974bf07a6845ba1c"
iuc
parents: 31
diff changeset
753 <param name="processmode" value="individual" />
8a7a42541080 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit cce7fcdd5e8ba8636c751f9f974bf07a6845ba1c"
iuc
parents: 31
diff changeset
754 <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"
iuc
parents: 31
diff changeset
755 <param name="input_bams" ftype="cram" value="freebayes-phix174.cram"/>
8a7a42541080 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit cce7fcdd5e8ba8636c751f9f974bf07a6845ba1c"
iuc
parents: 31
diff changeset
756 <param name="options_type_selector" value="simple"/>
34
a7c9782130e8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit be1c2e9e056710ef8b1110a121dc38c6e06dbbee"
iuc
parents: 33
diff changeset
757 <output name="output_vcf" file="freebayes-phix174-test1.vcf" lines_diff="6" />
32
8a7a42541080 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit cce7fcdd5e8ba8636c751f9f974bf07a6845ba1c"
iuc
parents: 31
diff changeset
758 </test>
23
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 22
diff changeset
759 </tests>
30
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
760 <help><![CDATA[
13
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devteam
parents:
diff changeset
761 **What it does**
2dd40b601766 Uploaded
devteam
parents:
diff changeset
762
2dd40b601766 Uploaded
devteam
parents:
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763 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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764
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765 See https://github.com/ekg/freebayes for details on FreeBayes.
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766
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767 ------
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768
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769 **Description**
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770
28
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771 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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772
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773 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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774
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775 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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776
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777 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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778
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779 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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780
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781 -------
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782
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783 **Galaxy-specific options**
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784
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785 Galaxy allows five levels of control over FreeBayes options, provided by the **Choose parameter selection level** menu option. These are:
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786
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787 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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788 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.
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789 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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790 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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791 5. *Complete list of all options*: Gives you full control by exposing all FreeBayes options as Galaxy parameters.
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792
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793 ------
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794
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795 **Command-line parameters**
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796
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797 **Input**::
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798
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799 --bam FILE The file or set of BAM files to be analyzed.
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800 --bam-list FILE A file containing a list of BAM files to be analyzed.
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801
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802 --stdin Read BAM input on stdin.
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803 --fasta-reference FILE Use FILE as the reference sequence for analysis.
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804 An index file (FILE.fai) will be created if none exists.
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805 If neither --targets nor --region are specified, FreeBayes
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806 will analyze every position in this reference.
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807 --targets FILE Limit analysis to targets listed in the BED-format FILE.
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808 --region <chrom>:<start>-<end> Limit analysis to the specified region, 0-base coordinates,
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809 end_position not included (same as BED format).
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810 Either '-' or '..' maybe used as a separator.
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811 --samples FILE Limit analysis to samples listed (one per line) in the FILE.
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812 By default FreeBayes will analyze all samples in its input
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813 BAM files.
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814 --populations FILE Each line of FILE should list a sample and a population which
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815 it is part of. The population-based bayesian inference model
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816 will then be partitioned on the basis of the populations.
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817 --cnv-map FILE Read a copy number map from the BED file FILE, which has
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818 either a sample-level ploidy:
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819 sample_name copy_number
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820 or a region-specific format:
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821 seq_name start end sample_name copy_number
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822 ... for each region in each sample which does not have the
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823 default copy number as set by --ploidy. These fields can be delimited
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824 by space or tab.
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825
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826 **Output**::
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827
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828 --vcf FILE Output VCF-format results to FILE. (default: stdout)
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829 --gvcf Write gVCF output, which indicates coverage in uncalled regions.
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830 --gvcf-chunk NUM When writing gVCF output emit a record for every NUM bases.
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831 --gvcf-dont-use-chunk When writing the gVCF output emit a record for all bases if
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832 set to "true" , will also route an int to --gvcf-chunk
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833 similar to --output-mode EMIT_ALL_SITES from GATK
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834 --variant-input VCF Use variants reported in VCF file as input to the algorithm.
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835 Variants in this file will included in the output even if
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836 there is not enough support in the data to pass input filters.
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837 --only-use-input-alleles Only provide variant calls and genotype likelihoods for sites
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838 and alleles which are provided in the VCF input, and provide
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839 output in the VCF for all input alleles, not just those which
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840 have support in the data.
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841 --haplotype-basis-alleles VCF When specified, only variant alleles provided in this input
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842 VCF will be used for the construction of complex or haplotype
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843 alleles.
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844 --report-all-haplotype-alleles At sites where genotypes are made over haplotype alleles,
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845 provide information about all alleles in output, not only
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846 those which are called.
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847 --report-monomorphic Report even loci which appear to be monomorphic, and report all
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848 considered alleles, even those which are not in called genotypes.
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849 Loci which do not have any potential alternates have '.' for ALT.
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850 --pvar N Report sites if the probability that there is a polymorphism
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851 at the site is greater than N. default: 0.0. Note that post-
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852 filtering is generally recommended over the use of this parameter.
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853 --strict-vcf Generate strict VCF format (FORMAT/GQ will be an int)
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854
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855 **Population model**::
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856
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857 --theta N The expected mutation rate or pairwise nucleotide diversity
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diff changeset
858 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
859 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
860 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
861 --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
862 --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
863 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
864 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
865 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
866 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
867 --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
868 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
869
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
870 **Reference allele**::
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
871
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
872 --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
873 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
874 --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
875 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
876
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
877 **Allele scope**::
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
878
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
879 --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
880 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
881 --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
882 --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
883 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
884 --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
885 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
886 --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
887 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
888 --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
889 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
890 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
891
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
892 **Indel realignment**::
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
893
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
894 --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
895
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
896 **Input filters**::
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
897
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
898 --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
899 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
900 --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
901 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
902 --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
903 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
904 --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
905 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
906 --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
907 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
908 --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
909 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
910 --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
911 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
912 default: ~unbounded
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
913 --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
914 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
915 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
916 --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
917 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
918 default: ~unbounded
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
919 --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
920 default: ~unbounded
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
921 --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
922 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
923 --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
924 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
925 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
926 --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
927 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
928 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
929 --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
930 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
931 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
932 --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
933 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
934 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
935 --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
936 --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
937 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
938 --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
939 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
940 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
941
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
942 **Population priors**::
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
943
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
944 --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
945 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
946
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
947 **Mappability priors**::
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
948
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
949 --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
950 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
951 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
952 --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
953 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
954 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
955 --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
956 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
957
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
958 **Genotype likelihoods**::
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
959
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
960 --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
961 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
962 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
963 --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
964 --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
965 --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
966 --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
967 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
968 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
969 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
970
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
971 **Algorithmic features**::
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
972
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
973 --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
974 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
975 --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
976 --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
977 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
978 --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
979 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
980 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
981 --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
982 --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
983 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
984 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
985 --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
986 --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
987 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
988 --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
989 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
990 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
991 --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
992 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
993
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
994 ------
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
995
25
bf27106652f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 24
diff changeset
996 **Acknowledgments**
13
2dd40b601766 Uploaded
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diff changeset
997
2dd40b601766 Uploaded
devteam
parents:
diff changeset
998 The initial version of the wrapper was produced by Dan Blankenberg and upgraded by Anton Nekrutenko.
28
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
999 TNG was developed by Bjoern Gruening.
30
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
1000 ]]>
23
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 22
diff changeset
1001 </help>
29
156b60c1530f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 99e8a87a2993ae644df15756044a40a42aa7a05b
iuc
parents: 28
diff changeset
1002 <expand macro="citations">
156b60c1530f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 99e8a87a2993ae644df15756044a40a42aa7a05b
iuc
parents: 28
diff changeset
1003 <citation type="bibtex">
156b60c1530f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 99e8a87a2993ae644df15756044a40a42aa7a05b
iuc
parents: 28
diff changeset
1004 @article{Tange2011a,
156b60c1530f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 99e8a87a2993ae644df15756044a40a42aa7a05b
iuc
parents: 28
diff changeset
1005 title = {GNU Parallel - The Command-Line Power Tool},
156b60c1530f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 99e8a87a2993ae644df15756044a40a42aa7a05b
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parents: 28
diff changeset
1006 author = {O. Tange},
156b60c1530f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 99e8a87a2993ae644df15756044a40a42aa7a05b
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parents: 28
diff changeset
1007 address = {Frederiksberg, Denmark},
156b60c1530f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 99e8a87a2993ae644df15756044a40a42aa7a05b
iuc
parents: 28
diff changeset
1008 journal = {;login: The USENIX Magazine},
156b60c1530f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 99e8a87a2993ae644df15756044a40a42aa7a05b
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parents: 28
diff changeset
1009 month = {Feb},
156b60c1530f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 99e8a87a2993ae644df15756044a40a42aa7a05b
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parents: 28
diff changeset
1010 number = {1},
156b60c1530f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 99e8a87a2993ae644df15756044a40a42aa7a05b
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parents: 28
diff changeset
1011 volume = {36},
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diff changeset
1012 url = {http://www.gnu.org/s/parallel},
156b60c1530f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 99e8a87a2993ae644df15756044a40a42aa7a05b
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diff changeset
1013 year = {2011},
156b60c1530f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 99e8a87a2993ae644df15756044a40a42aa7a05b
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parents: 28
diff changeset
1014 pages = {42-47}
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parents: 28
diff changeset
1015 }
156b60c1530f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 99e8a87a2993ae644df15756044a40a42aa7a05b
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parents: 28
diff changeset
1016 </citation>
156b60c1530f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 99e8a87a2993ae644df15756044a40a42aa7a05b
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parents: 28
diff changeset
1017 </expand>
13
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diff changeset
1018 </tool>