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1 <tool id="rgClean1" name="Clean genotypes:">
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2 <description>filter markers, subjects</description>
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3
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4 <command interpreter="python">
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5 rgClean.py '$input_file.extra_files_path' '$input_file.metadata.base_name' '$title' '$mind'
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6 '$geno' '$hwe' '$maf' '$mef' '$mei' '$out_file1' '$out_file1.files_path'
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7 '$relfilter' '$afffilter' '$sexfilter' '$fixaff'
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8 </command>
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9
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10 <inputs>
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11 <param name="input_file" type="data" label="RGenetics genotype library file in compressed Plink format"
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12 size="120" format="pbed" />
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13 <param name="title" type="text" size="80" label="Descriptive title for cleaned genotype file" value="Cleaned_data"/>
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14 <param name="geno" type="text" label="Maximum Missing Fraction: Markers" value="0.05" />
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15 <param name="mind" type="text" value="0.1" label="Maximum Missing Fraction: Subjects"/>
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16 <param name="mef" type="text" label="Maximum Mendel Error Rate: Family" value="0.05"/>
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17 <param name="mei" type="text" label="Maximum Mendel Error Rate: Marker" value="0.05"/>
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18 <param name="hwe" type="text" value="0" label="Smallest HWE p value (set to 0 for all)" />
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19 <param name="maf" type="text" value="0.01"
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20 label="Smallest Minor Allele Frequency (set to 0 for all)"/>
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21 <param name='relfilter' label = "Filter on pedigree relatedness" type="select"
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22 optional="false" size="132"
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23 help="Optionally remove related subjects if pedigree identifies founders and their offspring">
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24 <option value="all" selected='true'>No filter on relatedness</option>
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25 <option value="fo" >Keep Founders only (pedigree m/f ID = "0")</option>
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26 <option value="oo" >Keep Offspring only (one randomly chosen if >1 sibs in family)</option>
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27 </param>
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28 <param name='afffilter' label = "Filter on affection status" type="select"
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29 optional="false" size="132"
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30 help="Optionally remove affected or non affected subjects">
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31 <option value="allaff" selected='true'>No filter on affection status</option>
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32 <option value="affonly" >Keep Controls only (affection='1')</option>
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33 <option value="unaffonly" >Keep Cases only (affection='2')</option>
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34 </param>
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35 <param name='sexfilter' label = "Filter on gender" type="select"
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36 optional="false" size="132"
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37 help="Optionally remove all male or all female subjects">
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38 <option value="allsex" selected='true'>No filter on gender status</option>
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39 <option value="msex" >Keep Males only (pedigree gender='1')</option>
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40 <option value="fsex" >Keep Females only (pedigree gender='2')</option>
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41 </param>
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42 <param name="fixaff" type="text" value="0"
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43 label = "Change ALL subjects affection status to (0=no change,1=unaff,2=aff)"
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44 help="Use this option to switch the affection status to a new value for all output subjects" />
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45 </inputs>
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46
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47 <outputs>
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48 <data format="pbed" name="out_file1" metadata_source="input_file" label="${title}_rgClean.pbed" />
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49 </outputs>
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50
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51 <tests>
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52 <test>
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53 <param name='input_file' value='tinywga' ftype='pbed' >
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54 <metadata name='base_name' value='tinywga' />
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55 <composite_data value='tinywga.bim' />
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56 <composite_data value='tinywga.bed' />
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57 <composite_data value='tinywga.fam' />
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58 <edit_attributes type='name' value='tinywga' />
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59 </param>
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60 <param name='title' value='rgCleantest1' />
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61 <param name="geno" value="1" />
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62 <param name="mind" value="1" />
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63 <param name="mef" value="0" />
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64 <param name="mei" value="0" />
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65 <param name="hwe" value="0" />
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66 <param name="maf" value="0" />
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67 <param name="relfilter" value="all" />
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68 <param name="afffilter" value="allaff" />
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69 <param name="sexfilter" value="allsex" />
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70 <param name="fixaff" value="0" />
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71 <output name='out_file1' file='rgtestouts/rgClean/rgCleantest1.pbed' compare="diff" lines_diff="25" >
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72 <extra_files type="file" name='rgCleantest1.bim' value="rgtestouts/rgClean/rgCleantest1.bim" compare="diff" />
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73 <extra_files type="file" name='rgCleantest1.fam' value="rgtestouts/rgClean/rgCleantest1.fam" compare="diff" />
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74 <extra_files type="file" name='rgCleantest1.bed' value="rgtestouts/rgClean/rgCleantest1.bed" compare="diff" />
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75 </output>
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76 </test>
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77 </tests>
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78 <help>
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79
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80 .. class:: infomark
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81
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82 **Syntax**
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83
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84 - **Genotype data** is the input genotype file chosen from your current history
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85 - **Descriptive title** is the name to use for the filtered output file
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86 - **Missfrac threshold: subjects** is the threshold for missingness by subject. Subjects with more than this fraction missing will be excluded from the import
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87 - **Missfrac threshold: markers** is the threshold for missingness by marker. Markers with more than this fraction missing will be excluded from the import
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88 - **MaxMendel Individuals** Mendel error fraction above which to exclude subjects with more than the specified fraction of mendelian errors in transmission (for family data only)
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89 - **MaxMendel Families** Mendel error fraction above which to exclude families with more than the specified fraction of mendelian errors in transmission (for family data only)
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90 - **HWE** is the threshold for HWE test p values below which the marker will not be imported. Set this to -1 and all markers will be imported regardless of HWE p value
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91 - **MAF** is the threshold for minor allele frequency - SNPs with lower MAF will be excluded
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92 - **Filters** for founders/offspring or affected/unaffected or males/females are optionally available if needed
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93 - **Change Affection** is only needed if you want to change the affection status for creating new analysis datasets
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94
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95 -----
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96
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97 **Attribution**
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98
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99 This tool relies on the work of many people. It uses Plink http://pngu.mgh.harvard.edu/~purcell/plink/,
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100 and the R http://cran.r-project.org/ and
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101 Bioconductor http://www.bioconductor.org/ projects.
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102 respectively.
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103
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104 In particular, http://pngu.mgh.harvard.edu/~purcell/plink/
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105 has excellent documentation describing the parameters you can set here.
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106
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107 This implementation is a Galaxy tool wrapper around these third party applications.
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108 It was originally designed and written for family based data from the CAMP Illumina run of 2007 by
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109 ross lazarus (ross.lazarus@gmail.com) and incorporated into the rgenetics toolkit.
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110
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111 Rgenetics merely exposes them, wrapping Plink so you can use it in Galaxy.
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112
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113 -----
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114
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115 **Summary**
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116
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117 Reliable statistical inference depends on reliable data. Poor quality samples and markers
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118 may add more noise than signal, decreasing statistical power. Removing the worst of them
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119 can be done by setting thresholds for some of the commonly used technical quality measures
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120 for genotype data. Of course discordant replicate calls are also very informative but are not
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121 in scope here.
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122
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123 Marker cleaning: Filters are available to remove markers below a specific minor allele
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124 frequency, beyond a Hardy Wienberg threshold, below a minor allele frequency threshold,
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125 or above a threshold for missingness. If family data are available, thresholds for Mendelian
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126 error can be set.
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127
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128 Subject cleaning: Filters are available to remove subjects with many missing calls. Subjects and markers for family data can be filtered by proportions
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129 of Mendelian errors in observed transmission. Use the QC reporting tool to
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130 generate a comprehensive series of reports for quality control.
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131
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132 Note that ancestry and cryptic relatedness should also be checked using the relevant tools.
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133
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134 -----
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135
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136 .. class:: infomark
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137
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138 **Tip**
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139
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140 You can check that you got what you asked for by running the QC tool to ensure that the distributions
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141 are truncated the way you expect. Note that you do not expect that the thresholds will be exactly
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142 what you set - some bad assays and subjects are out in multiple QC measures, so you sometimes have
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143 more samples or markers than you exactly set for each threshold. Finally, the ordering of
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144 operations matters and Plink is somewhat restrictive about what it will do on each pass
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145 of the data. At least it's fixed.
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146
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147 -----
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148
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149 This Galaxy tool was written by Ross Lazarus for the Rgenetics project
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150 It uses Plink for most calculations - for full Plink attribution, source code and documentation,
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151 please see http://pngu.mgh.harvard.edu/~purcell/plink/ plus some custom python code
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152
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153 </help>
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154 </tool>
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