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1 <tool id="rgLDIndep1" name="LD Independent:">
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2 <code file="rgLDIndep_code.py"/>
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3
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4 <description>filter high LD pairs - decrease redundancy</description>
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5
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6 <command interpreter="python">
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7 rgLDIndep.py '$input_file.extra_files_path' '$input_file.metadata.base_name' '$title1' '$mind'
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8 '$geno' '$hwe' '$maf' '$mef' '$mei' '$out_file1'
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9 '$out_file1.files_path' '$window' '$step' '$r2'
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10 </command>
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11
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12 <inputs>
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13 <param name="input_file" type="data" label="RGenetics genotype data from your current history"
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14 size="80" format="pbed" />
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15 <param name="title1" type="text" size="80" label="Descriptive title for cleaned genotype file" value="LD_Independent"/>
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16 <param name="r2" type="float" value = "0.1"
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17 label="r2 threshold: Select only pairs at or below this r^2 threshold (eg 0.1)"
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18 help="LD threshold defining LD independent markers" />
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19 <param name="window" type="integer" value = "40" label="Window: Window size to limit LD pairwise"
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20 help = "Bigger is better but time taken blows up exponentially as the window grows!" />
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21 <param name="step" type="integer" value = "30" label="Step: Move window this far and recompute"
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22 help = "Smaller is better but of course, time increases..." />
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23 <param name="geno" type="float" label="Maximum Missing Fraction: Markers" value="1.0" />
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24 <param name="mind" type="float" value="1.0" label="Maximum Missing Fraction: Subjects"/>
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25 <param name="mef" type="float" label="Maximum Mendel Error Rate: Family" value="1.0"/>
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26 <param name="mei" type="float" label="Maximum Mendel Error Rate: Marker" value="1.0"/>
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27 <param name="hwe" type="float" value="0.0" label="Smallest HWE p value (set to 0 for all)" />
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28 <param name="maf" type="float" value="0.0"
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29 label="Smallest Allowable Minor Allele Frequency (set to 0.0 for all)"/>
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30
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31 </inputs>
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32
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33 <outputs>
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34 <data format="pbed" name="out_file1" metadata_source="input_file" />
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35 </outputs>
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36 <tests>
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37 <test>
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38
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39 <param name='input_file' value='tinywga' ftype='pbed' >
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40 <metadata name='base_name' value='tinywga' />
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41 <composite_data value='tinywga.bim' />
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42 <composite_data value='tinywga.bed' />
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43 <composite_data value='tinywga.fam' />
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44 <edit_attributes type='name' value='tinywga' />
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45 </param>
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46 <param name='title1' value='rgLDIndeptest1' />
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47 <param name="mind" value="1" />
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48 <param name="geno" value="1" />
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49 <param name="hwe" value="0" />
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50 <param name="maf" value="0" />
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51 <param name="mef" value="1" />
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52 <param name="mei" value="1" />
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53 <param name="window" value="10000" />
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54 <param name="step" value="5000" />
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55 <param name="r2" value="0.1" />
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56 <output name='out_file1' file='rgtestouts/rgLDIndep/rgLDIndeptest1.pbed' ftype='pbed' compare="diff" lines_diff='7'>
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57 <extra_files type="file" name='rgLDIndeptest1.bim' value="rgtestouts/rgLDIndep/rgLDIndeptest1.bim" compare="sim_size" delta="1000"/>
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58 <extra_files type="file" name='rgLDIndeptest1.fam' value="rgtestouts/rgLDIndep/rgLDIndeptest1.fam" compare="diff" />
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59 <extra_files type="file" name='rgLDIndeptest1.bed' value="rgtestouts/rgLDIndep/rgLDIndeptest1.bed" compare="sim_size" delta = "1000" />
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60 </output>
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61 </test>
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62 </tests>
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63 <help>
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64
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65 .. class:: infomark
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66
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67 **Attribution**
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68
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69 This tool relies on Plink from Shaun Purcell. For full documentation, please see his web site
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70 at http://pngu.mgh.harvard.edu/~purcell/plink/ where there is excellent documentation describing
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71 the parameters you can set here.
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72
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73 Rgenetics merely exposes them, wrapping Plink so you can use it in Galaxy.
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74
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75 **Summary**
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76
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77 In addition to filtering some marker and sample quality measures,
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78 this tool reduces the amount of overlapping information, by removing
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79 most of the duplicate information contained in linkage disequilibrium. This is
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80 a lossy process and for some methods, signal may be lost. However, this makes
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81 the dataset far more compact (eg 10% of the original storage size) while still
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82 being highly informative and less biased for some (note NOT all!) statistical methods.
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83 This is the Clean tool with additional data reduction via Plink LD pruning.
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84 Use the Clean tool if you don't want LD pruning - which you don't for most statistical testing.
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85 For ancestry and relatedness, you may well want LD pruned data as it has
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86 some specific desirable properties.
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87
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88 **LD**
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89
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90 Pairwise Linkage disequilibrium (LD) measures the extent to which the genotype at one locus
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91 predicts the state of another locus at the level of an entire population.
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92 When population LD between a pair of markers is high,
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93 knowing an individual's genotype at one locus allows confident prediction of the genotype at the other.
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94 In other words, high LD means information redundancy between markers. For some
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95 purposes, removing some of this redundancy can improve the performance of some analyses.
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96 Executing this tool will create a new genotype dataset in your current history containing
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97 LD independent markers - most of the genetic information is retained but without as much redundancy.
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98
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99 Set a pairwise LD threshold (eg r^2 = 0.2) and the (smaller) resulting dataset will have no
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100 pairs of marker with r^2 greater than 0.2. Additional filters are available to remove markers
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101 below a specific minor allele frequency, or above a specific level of missingness,
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102 and to remove subjects using similar criteria. Subjects and markers for family data can be
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103 filtered by proportions of Mendelian errors in observed transmission.
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104
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105 -----
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106
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107 **Syntax**
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108
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109 - **Genotype data** is the input pedfile chosen from available library files
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110 - **New name** is the name to use for the filtered output file
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111 - **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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112 - **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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113 - **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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114 - **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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115 - **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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116 - **MAF** is the threshold for minor allele frequency - SNPs with lower MAF will be excluded
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117 - **r^2** is the pairwise LD threshold as r^2. Lower -> less marker redundancy -> fewer markers
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118 - **Window** is the window width for LD threshold. Bigger -> slower -> more complete
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119 - **Skip** is the distance to move the window along the genome. Should be window or less.
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120
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121 -----
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122
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123 **Disclaimer**
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124
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125 This tool relies on Plink from Shaun Purcell. For full documentation, please see his web site
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126 at http://pngu.mgh.harvard.edu/~purcell/plink/ where thereis excellent documentation describing
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127 the parameters you can set here. Rgenetics merely exposes them, and wraps Plink so you can use it in Galaxy.
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128
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129 This tool is designed to create genotype data files with more or less LD independent sets of markers. These
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130 reduced genotype data files are particularly useful for purposes such as evaluating
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131 ancestry (eg eigenstrat) or relatedness (eg rgGRR)
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132
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133 LD pruning decreases redundancy among the genotype data by removing one of each pair of markers
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134 in strong LD (above the r^2 threshold) over successive genomic windows (the Window parameter),
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135 skipping (the Skip parameter bases between windows. The defaults should produce useable outputs.
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136
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137 This might be more efficient for rgGRR and
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138 eigenstrat...The core quote is
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139
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140 "This generates the same output files as the first version;
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141 the only difference is that a simple pairwise threshold is used.
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142 The first two parameters (50 and 5) are the same as above (window size and step);
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143 the third parameter represents the r^2 threshold.
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144 Note: this represents the pairwise SNP-SNP metric now, not the
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145 multiple correlation coefficient; also note, this is based on the
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146 genotypic correlation, i.e. it does not involve phasing.
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147 "
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148
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149 -----
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150
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151
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152
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153 This Galaxy tool was written by Ross Lazarus for the Rgenetics project
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154 It uses Plink for most calculations - for full Plink attribution, source code and documentation,
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155 please see http://pngu.mgh.harvard.edu/~purcell/plink/ plus some custom python code
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156
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157 </help>
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158 </tool>
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