Mercurial > repos > iuc > gemini_burden

annotate gemini_burden.xml @ 8:f0bf88e9e689 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit f7bdf08922aaf4119aefe7041e754a69cf64aebd
author iuc
date Wed, 13 Jul 2022 15:28:45 +0000
parents 699ce2631e79
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1 <tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@">
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2 <description>perform sample-wise gene-level burden calculations</description>
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3 <expand macro="bio_tools"/>
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4 <macros>
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5 <import>gemini_macros.xml</import>
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6 <token name="@BINARY@">burden</token>
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7 <token name="@GEMINI_BUG_WARNING@">Caveat: due to a bug in this version of GEMINI, filtering on alternate allele frequency will get disabled when you select 'All non-synonymous variants' as the types of variants to be used for the burden calculations above.</token>
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8 </macros>
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9 <expand macro="requirements" />
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10 <expand macro="stdio" />
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11 <expand macro="version_command" />
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12 <command>
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13 <![CDATA[
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14 gemini @BINARY@
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15 $nonsynonymous
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16 #if str($analysis.mode) == "c-alpha":
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17 --calpha
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18 #if str($analysis.casecontrol.source) == "custom":
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19 --cases
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20 #echo (" ".join("'" + token + "'" for token in $analysis.casecontrol.cases.strip().split()))#
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21 --controls
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22 #echo (" ".join("'" + token + "'" for token in $analysis.casecontrol.controls.strip().split()))#
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23 #end if
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24 --min-aaf ${analysis.min_aaf}
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25 --max-aaf ${analysis.max_aaf}
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26 --permutations ${analysis.permutations}
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27 ${analysis.save_tscores}
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28 #end if
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29 '$infile'
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30 > '$outfile'
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31 #if str($analysis.mode) == "c-alpha" and $analysis.save_tscores:
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32 && touch permutated_t_scores.txt
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33 && mv permutated_t_scores.txt $t_scores
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34 #end if
0
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35 ]]>
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36
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37 </command>
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38 <inputs>
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39 <expand macro="infile" />
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40 <param argument="--non-synonymous" name="nonsynonymous" type="select"
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41 label="Use the following types of variants for the burden calculation">
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42 <option value="">High impact variants only</option>
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43 <option value="--nonsynonymous">All non-synonymous variants</option>
0
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44 </param>
4
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45 <conditional name="analysis">
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46 <param argument="--calpha" name="mode" type="select"
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47 label="Which type of burden calculation should be performed?">
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48 <option value="counts">Count of variants per gene and sample</option>
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49 <option value="c-alpha">C-alpha association test per gene</option>
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50 </param>
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51 <when value="counts" />
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52 <when value="c-alpha">
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53 <conditional name="casecontrol">
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54 <param name="source" type="select"
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55 label="Selection of case and control samples"
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56 help="Specify how case and control samples for the C-alpha association test should be selected">
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57 <option value="ped">Use PED file information</option>
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58 <option value="custom">Custom selection</option>
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59 </param>
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60 <when value="ped" />
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61 <when value="custom">
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62 <param argument="--cases" name="cases" type="text" value=""
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63 label="Space separated list of cases for association testing"/>
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64 <param argument="--controls" name="controls" type="text" value=""
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65 label="Space separated list of controls for association testing" help="(--controls)"/>
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66 </when>
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67 </conditional>
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68 <param argument="--min-aaf" name="min_aaf" type="float" min="0" max="1" value="0"
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69 label="The min. alt. allele frequency for a variant to be included"
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70 help="@GEMINI_BUG_WARNING@" />
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71 <param argument="--max-aaf" name="max_aaf" type="float" min="0" max="1" value="1"
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72 label="The max. alt. allele frequency for a variant to be included"
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73 help="@GEMINI_BUG_WARNING@" />
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74 <param argument="--permutations" name="permutations" type="integer" min="1" value="100" label="Number of permutations to run for the C-alpha test" />
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75 <param argument="--save_tscores" name="save_tscores" type="boolean" truevalue="--save_tscores" falsevalue="" checked="False"
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76 label="Save the list of individual T-scores from all permutations as an extra dataset" />
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77 </when>
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78 </conditional>
0
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79 </inputs>
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80 <outputs>
4
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81 <data name="outfile" format="tabular"
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82 label="GEMINI burden ${analysis.mode} on ${on_string}" />
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83 <data name="t_scores" format="tabular"
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84 label="GEMINI burden permuted T scores on ${on_string}">
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85 <filter>analysis['mode'] == 'c-alpha' and analysis['save_tscores']</filter>
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86 </data>
0
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87 </outputs>
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88 <tests>
4
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89 <test expect_num_outputs="1">
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90 <!-- test counts mode with defaults -->
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91 <param name="infile" value="gemini_de_novo_input.db" ftype="gemini.sqlite" />
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92 <conditional name="analysis">
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93 <param name="mode" value="counts" />
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94 </conditional>
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95 <output name="outfile" file="gemini_burden_count_highimpact_result.tabular" />
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96 </test>
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97 <test expect_num_outputs="1">
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98 <!-- test nonsynonymous parameter -->
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99 <param name="infile" value="gemini_de_novo_input.db" ftype="gemini.sqlite" />
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100 <param name="nonsynonymous" value="--nonsynonymous" />
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101 <conditional name="analysis">
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102 <param name="mode" value="counts" />
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103 </conditional>
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104 <output name="outfile" file="gemini_burden_count_nonsynonymous_result.tabular" />
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105 </test>
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106 <test expect_num_outputs="1">
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107 <!-- test c-alpha mode with defaults -->
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108 <param name="infile" value="gemini_de_novo_input.db" ftype="gemini.sqlite" />
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109 <conditional name="analysis">
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110 <param name="mode" value="c-alpha" />
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111 <conditional name="casecontrol">
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112 <param name="source" value="ped" />
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113 </conditional>
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114 </conditional>
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115 <output name="outfile" file="gemini_burden_calpha_template.tabular" compare="re_match" />
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116 </test>
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117 <test expect_num_outputs="1">
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118 <!-- test c-alpha mode with user-supplied case/control samples -->
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119 <param name="infile" value="gemini_de_novo_input.db" ftype="gemini.sqlite" />
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120 <conditional name="analysis">
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121 <param name="mode" value="c-alpha" />
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122 <conditional name="casecontrol">
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123 <param name="source" value="custom" />
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124 <param name="controls" value="1_kid 3_kid" />
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125 <param name="cases" value="1_dad 1_mom 3_dad 3_mom" />
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126 </conditional>
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127 </conditional>
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128 <output name="outfile" file="gemini_burden_calpha_template.tabular" compare="re_match" />
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129 </test>
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130 <test expect_num_outputs="2">
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131 <!-- test additional T scores output generation -->
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132 <param name="infile" value="gemini_de_novo_input.db" ftype="gemini.sqlite" />
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133 <conditional name="analysis">
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134 <param name="mode" value="c-alpha" />
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135 <conditional name="casecontrol">
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136 <param name="source" value="custom" />
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137 <param name="controls" value="1_kid 3_kid" />
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138 <param name="cases" value="1_dad 1_mom 3_dad 3_mom" />
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139 </conditional>
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140 <param name="permutations" value="2" />
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141 <param name="save_tscores" value="True" />
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142 </conditional>
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143 <output name="t_scores">
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144 <assert_contents>
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145 <has_line_matching expression="WDR37&#009;.+&#009;.+" />
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146 </assert_contents>
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147 </output>
0
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148 </test>
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149 </tests>
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150 <help><![CDATA[
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151 **What it does**
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152
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153 Burden performs sample-wise gene-level burden calculations.
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154
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155 The burden tool provides a set of utilities to perform burden summaries on a per-gene, per sample basis. By default, it outputs a table of gene-wise counts of all high impact variants in coding regions for each sample:
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156
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157 GEMINI burden example::
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158
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159 gene M10475 M10478 M10500 M128215
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160 WDR37 2 2 2 2
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161 CTBP2 0 0 0 1
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162 DHODH 1 0 0 0
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163
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164 **Setting examples**
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165
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166 **--nonsynonymous**
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167
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168 If you want to be a little bit less restrictive, you can include all non-synonymous variants instead.
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169
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170 GEMINI output with setting --nonsynonymous::
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171
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172 gene M10475 M10478 M10500 M128215
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173 SYCE1 0 1 1 0
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174 WDR37 2 2 2 2
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175 CTBP2 0 0 0 1
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176 ASAH2C 2 1 1 0
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177 DHODH 1 0 0 0
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178
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179 **--calpha**
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180
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181 If your database has been loaded with a PED file describing case and control samples, you can calculate the c-alpha statistic for cases vs. control.
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182
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183 GEMINI output with setting --calpha::
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184
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185 gene T c Z p_value
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186 SYCE1 -0.5 0.25 -1.0 0.841344746069
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187 WDR37 -1.0 1.5 -0.816496580928 0.792891910879
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188 CTBP2 0.0 0.0 nan nan
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189 ASAH2C -0.5 0.75 -0.57735026919 0.718148569175
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190 DHODH 0.0 0.0 nan nan
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191
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192 To calculate the **P-value** using a permutation test, use the --permutations option, specifying the number of permutations of the case/control labels you want to use.
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193
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194 **--min-aaf and --max-aaf for --calpha**
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195
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196 By default, all variants affecting a given gene will be included in the C-alpha computation. However, one may establish alternate allele frequency boundaries for the variants included using the --min-aaf and --max-aaf options.
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197
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198 Used settings:
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199
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200 - -calpha test.burden.db
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201 - -min-aaf 0.0
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202 - -max-aaf 0.01
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203 - -cases
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204 - -controls for --calpha
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205
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206 If you do not have a PED file loaded, or your PED file does not follow the standard PED phenotype encoding format you can still perform the c-alpha test, but you have to specify which samples are the control samples and which are the case samples.
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207
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208 Used settings:
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209
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210 - -controls M10475 M10478
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211 - -cases M10500 M128215
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212 - -calpha
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213
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214 Output::
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215
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216 gene T c Z p_value
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217 SYCE1 -0.5 0.25 -1.0 0.841344746069
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218 WDR37 -1.0 1.5 -0.816496580928 0.792891910879
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219 CTBP2 0.0 0.0 nan nan
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220 ASAH2C -0.5 0.75 -0.57735026919 0.718148569175
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221 DHODH 0.0 0.0 nan nan
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222
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223 **--nonsynonymous --calpha**
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224
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225 If you would rather consider all nonsynonymous variants for the C-alpha test rather than just the medium and high impact variants, add the --nonsynonymous flag.
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226
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227
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228 ]]></help>
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229 <expand macro="citations">
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230 <citation type="doi">10.1371/journal.pgen.1001322</citation><!-- c-alpha citation -->
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231 </expand>
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232 </tool>