Mercurial > repos > iuc > bcftools_csq

annotate bcftools_csq.xml @ 13:ae68ceb4cca3 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit cdb4558db96dd58f9f85267488a1e27ad813fca4
author iuc
date Thu, 29 Sep 2022 08:51:18 +0000
parents 6c790a091c7c
children d237eaef451f
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1 <?xml version='1.0' encoding='utf-8'?>
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2 <tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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3 <description>Haplotype aware consequence predictor</description>
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4 <macros>
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5 <token name="@EXECUTABLE@">csq</token>
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6 <import>macros.xml</import>
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7 </macros>
9
68216882a410 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit af43d9cf6824f88726900857116f333ff4cdd336"
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8 <expand macro="bio_tools" />
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9 <expand macro="requirements">
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10 <expand macro="samtools_requirement"/>
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11 </expand>
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12 <expand macro="version_command" />
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13 <command detect_errors="aggressive"><![CDATA[
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14 @PREPARE_ENV@
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15 @PREPARE_INPUT_FILE@
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16 #set $section = $sec_required.reference_source
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17 @PREPARE_FASTA_REF@
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19 #set $section = $sec_restrict
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20 @PREPARE_TARGETS_FILE@
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21 @PREPARE_REGIONS_FILE@
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23 bcftools @EXECUTABLE@
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25 ## csq required inputs section
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26 #set $section = $sec_required.reference_source
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27 @FASTA_REF@
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28 --gff-annot '$sec_required.gff_annot'
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30 ## csq options section
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31 #if str($sec_csq_opts.ncsq):
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32 --ncsq $sec_csq_opts.ncsq
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33 #end if
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34 $sec_csq_opts.local_csq
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35 #if $sec_csq_opts.phase:
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36 --phase $sec_csq_opts.phase
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37 #end if
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38 #if str($sec_csq_opts.custom_tag):
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39 --custom-tag '$sec_csq_opts.custom_tag'
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40 #end if
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41 #if str($sec_csq_opts.trim_protein_seq)
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42 --trim-protein-seq $sec_csq_opts.trim_protein_seq
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43 #end if
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44
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45 ## Subset section
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46 #set $section = $sec_subset
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47 @SAMPLES@
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48
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49 ## Filter section
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50 #set $section = $sec_restrict
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51 @INCLUDE@
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52 @EXCLUDE@
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53 @REGIONS@
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54 @TARGETS@
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55
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56 @OUTPUT_TYPE@
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57
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58 ## Primary Input/Outputs
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59 @INPUT_FILE@
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60 > '$output_file'
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61
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62 ]]>
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63 </command>
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64 <inputs>
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65 <expand macro="macro_input" />
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66 <section name="sec_required" expanded="true" title="Required References">
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67 <expand macro="macro_fasta_ref" />
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68 <param name="gff_annot" type="data" format="gff3" label="GFF3 annotation file"
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69 help="From Ensembl: ftp://ftp.ensembl.org/pub/current_gff3/"/>
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70 </section>
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71 <section name="sec_csq_opts" expanded="true" title="CSQ Options">
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72 <param name="ncsq" type="integer" value="16" min="1" max="50" label="maximum number of consequences to consider per site"
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73 help="-ncsq 16"/>
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74 <param name="local_csq" type="boolean" truevalue="--local-csq" falsevalue="" checked="false" label="run localized predictions considering only one VCF record at a time"
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75 help="--local-csq switch off haplotype-aware calling, run localized predictions considering only one VCF record at a time"/>
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76 <param name="phase" type="select" optional="true" label="phase"
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77 help="how to construct haplotypes and how to deal with unphased data">
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78 <option value="a">take GTs as is, create haplotypes regardless of phase (0/1 -> 0|1)</option>
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79 <option value="m">merge *all* GTs into a single haplotype (0/1 -> 1, 1/2 -> 1)</option>
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80 <option value="r">require phased GTs, throw an error on unphased het GTs</option>
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81 <option value="R">create non-reference haplotypes if possible (0/1 -> 1|1, 1/2 -> 1|2)</option>
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82 <option value="s">skip unphased GTs</option>
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83 </param>
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84 <param name="custom_tag" type="text" value="" optional="true"
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85 label="use this custom tag to store consequences rather than the default BCSQ tag">
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86 <validator type="regex" message="">^(\w+)?$</validator>
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87 </param>
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88 <param argument="--trim-protein-seq" type="integer" min="0" value="" optional="true" label="Abbreviate protein-changing predictions"
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89 help="Abbreviate protein-changing predictions to max INT aminoacids" />
0
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90 </section>
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91
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92 <section name="sec_restrict" expanded="false" title="Restrict to">
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93 <expand macro="macro_restrict" />
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94 <expand macro="macro_restrict" type="target" label_type="Target" />
0
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95 <expand macro="macro_include" />
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96 <expand macro="macro_exclude" />
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97 </section>
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98 <section name="sec_subset" expanded="false" title="Subset Options">
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99 <expand macro="macro_samples" />
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100 </section>
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101 <expand macro="macro_select_output_type" />
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102 </inputs>
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103 <outputs>
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104 <expand macro="macro_vcf_output" />
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105 </outputs>
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106 <tests>
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107 <test>
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108 <param name="input_file" ftype="vcf" value="csq.vcf" />
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109 <expand macro="test_using_reference" ref="csq.fa" />
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110 <param name="gff_annot" ftype="gff3" value="csq.gff3" />
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111 <param name="output_type" value="v" />
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112 <output name="output_file">
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113 <assert_contents>
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114 <has_text text="BCSQ" />
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115 </assert_contents>
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116 </output>
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117 </test>
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118 <test>
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119 <param name="input_file" ftype="vcf" value="csq.vcf" />
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120 <expand macro="test_using_reference" select_from="cached" ref="csq" />
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121 <param name="gff_annot" ftype="gff3" value="csq.gff3" />
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122 <param name="output_type" value="v" />
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123 <output name="output_file">
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124 <assert_contents>
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125 <has_text text="BCSQ" />
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126 </assert_contents>
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127 </output>
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128 </test>
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129 <!-- Test protein seq prediction-->
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130 <test>
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131 <param name="input_file" ftype="vcf" value="csq.vcf" />
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132 <expand macro="test_using_reference" select_from="cached" ref="csq" />
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133 <param name="gff_annot" ftype="gff3" value="csq.gff3" />
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134 <param name="output_type" value="v" />
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135 <section name="sec_csq_opts">
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136 <param name="trim_protein_seq" value="10"/>
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137 </section>
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138 <output name="output_file">
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139 <assert_contents>
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140 <has_text text="BCSQ" />
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141 </assert_contents>
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142 </output>
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143 <assert_command>
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144 <has_text text="--trim-protein-seq" />
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145 </assert_command>
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146 </test>
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147 <!-- Test region overlap-->
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148 <test>
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149 <param name="input_file" ftype="vcf" value="csq.vcf" />
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150 <expand macro="test_using_reference" select_from="cached" ref="csq" />
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151 <param name="gff_annot" ftype="gff3" value="csq.gff3" />
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152 <param name="output_type" value="v" />
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153 <section name="sec_restrict">
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154 <param name="regions_overlap" value="1"/>
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155 </section>
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156 <output name="output_file">
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157 <assert_contents>
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158 <has_text text="BCSQ" />
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159 </assert_contents>
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160 </output>
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161 <assert_command>
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162 <has_text text="--regions-overlap" />
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163 </assert_command>
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164 </test>
0
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165 </tests>
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166 <help><![CDATA[
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167 =====================================
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168 bcftools @EXECUTABLE@
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169 =====================================
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170
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171 Haplotype aware consequence predictor which correctly handles combined variants such as MNPs split over
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172 multiple VCF records, SNPs separated by an intron (but adjacent in the spliced transcript) or nearby
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173 frame-shifting indels which in combination in fact are not frame-shifting.
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174
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175 The output VCF is annotated with INFO/BCSQ and FORMAT/BCSQ tag (configurable with the -c option).
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176 The latter is a bitmask of indexes to INFO/BCSQ, with interleaved haplotypes. See the usage examples
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177 below for using the %TBCSQ converter in query for extracting a more human readable form from this bitmask.
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178 The contruction of the bitmask limits the number of consequences that can be referenced in the FORMAT/BCSQ tags.
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179 By default this is 16, but if more are required, see the --ncsq option.
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180
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181 The program requires on input a VCF/BCF file, the reference genome in fasta format (--fasta-ref)
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182 and genomic features in the GFF3 format downloadable from the Ensembl website (--gff-annot),
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183 and outputs an annotated VCF/BCF file. Currently, only Ensembl GFF3 files are supported.
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184
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185 By default, the input VCF should be phased. If phase is unknown, or only partially known,
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186 the --phase option can be used to indicate how to handle unphased data. Alternatively,
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187 haplotype aware calling can be turned off with the --local-csq option.
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188
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189 If conflicting (overlapping) variants within one haplotype are detected, a warning will
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190 be emitted and predictions will be based on only the first variant in the analysis.
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191
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192 Symbolic alleles are not supported. They will remain unannotated in the output VCF and are
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193 ignored for the prediction analysis.
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194
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195
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196 @REGIONS_HELP@
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197 @TARGETS_HELP@
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198
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199 @BCFTOOLS_MANPAGE@#@EXECUTABLE@
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200
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201 @BCFTOOLS_WIKI@
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202 ]]>
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203 </help>
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204 <expand macro="citations" />
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205 </tool>