Mercurial > repos > miller-lab > genome_diversity
annotate phylogenetic_tree.xml @ 39:e56023008e36 default tip
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author | miller-lab |
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date | Mon, 06 Jul 2015 10:32:24 -0400 |
parents | a631c2f6d913 |
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1 <tool id="gd_phylogenetic_tree" name="Phylogenetic Tree" version="1.1.0"> |
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2 <description>: Show genetic relationships among individuals</description> |
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3 |
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4 <command interpreter="python"> |
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5 #import json |
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6 #import base64 |
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7 #import zlib |
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8 #set $ind_names = $input.dataset.metadata.individual_names |
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9 #set $ind_colms = $input.dataset.metadata.individual_columns |
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10 #set $ind_dict = dict(zip($ind_names, $ind_colms)) |
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11 #set $ind_json = json.dumps($ind_dict, separators=(',',':')) |
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12 #set $ind_comp = zlib.compress($ind_json, 9) |
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13 #set $ind_arg = base64.b64encode($ind_comp) |
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14 phylogenetic_tree.py '$input' '$output' '$output.files_path' |
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15 #if $input_type.choice == '0' |
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16 'gd_snp' |
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17 #if $input_type.data_source.choice == '0' |
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18 'sequence_coverage' |
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19 '$input_type.data_source.minimum_coverage' |
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20 '$input_type.data_source.minimum_quality' |
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21 #else if $input_type.data_source.choice == '1' |
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22 'estimated_genotype' '0' '0' |
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23 #end if |
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24 #else if $input_type.choice == '1' |
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25 'gd_genotype' 'estimated_genotype' '0' '0' |
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26 #end if |
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27 #if $individuals.choice == '0' |
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28 'all_individuals' |
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29 #else if $individuals.choice == '1' |
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30 '$individuals.p1_input' |
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31 #end if |
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32 #if ((str($input.metadata.scaffold) == str($input.metadata.ref)) and (str($input.metadata.pos) == str($input.metadata.rPos))) or (str($include_reference) == '0') |
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33 'none' |
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34 #else |
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35 '$input.metadata.dbkey' |
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36 #end if |
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37 #set $draw_tree_options = ''.join(str(x) for x in [$branch_style, $scale_style, $length_style, $layout_style]) |
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38 #if $draw_tree_options == '' |
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39 '' |
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40 #else |
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41 '-$draw_tree_options' |
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42 #end if |
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43 '$ind_arg' |
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44 </command> |
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45 |
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46 <inputs> |
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47 <conditional name="input_type"> |
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48 <param name="choice" type="select" format="integer" label="Input format"> |
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49 <option value="0" selected="true">gd_snp</option> |
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50 <option value="1">gd_genotype</option> |
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51 </param> |
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52 <when value="0"> |
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53 <param name="input" type="data" format="gd_snp" label="SNP dataset" /> |
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54 |
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55 <conditional name="data_source"> |
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56 <param name="choice" type="select" format="integer" label="Distance metric"> |
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57 <option value="0">sequence coverage</option> |
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58 <option value="1" selected="true">estimated genotype</option> |
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59 </param> |
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60 <when value="0"> |
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61 <param name="minimum_coverage" type="integer" min="0" value="0" label="Minimum SNP coverage" /> |
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62 <param name="minimum_quality" type="integer" min="0" value="0" label="Minimum SNP quality" |
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63 help="Note: minimum coverage and minimum quality cannot both be 0" /> |
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64 </when> |
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65 <when value="1"/> |
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66 </conditional> |
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67 </when> |
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68 <when value="1"> |
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69 <param name="input" type="data" format="gd_genotype" label="Genotype dataset" /> |
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70 </when> |
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71 </conditional> |
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72 |
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73 <conditional name="individuals"> |
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74 <param name="choice" type="select" label="Compute for"> |
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75 <option value="0" selected="true">All individuals</option> |
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76 <option value="1">Individuals in a population</option> |
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77 </param> |
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78 <when value="0" /> |
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79 <when value="1"> |
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80 <param name="p1_input" type="data" format="gd_indivs" label="Population individuals" /> |
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81 </when> |
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82 </conditional> |
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83 |
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84 <param name="include_reference" type="select" format="integer" label="Include reference sequence"> |
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85 <option value="1" selected="true">Yes</option> |
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86 <option value="0">No</option> |
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87 </param> |
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88 |
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89 <param name="branch_style" type="select" display="radio"> |
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90 <label>Branch type</label> |
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91 <option value="" selected="true">square</option> |
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92 <option value="d">diagonal</option> |
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93 </param> |
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94 |
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95 <param name="scale_style" type="select" display="radio"> |
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96 <label>Draw branches to scale</label> |
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97 <option value="" selected="true">yes</option> |
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98 <option value="s">no</option> |
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99 </param> |
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100 |
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101 <param name="length_style" type="select" display="radio"> |
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102 <label>Show branch lengths</label> |
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103 <option value="" selected="true">yes</option> |
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104 <option value="b">no</option> |
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105 </param> |
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106 |
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107 <param name="layout_style" type="select" display="radio"> |
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108 <label>Tree layout</label> |
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109 <option value="" selected="true">horizontal</option> |
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110 <option value="v">vertical</option> |
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111 </param> |
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112 </inputs> |
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113 |
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114 <outputs> |
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115 <data name="output" format="html" /> |
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116 </outputs> |
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117 |
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118 <tests> |
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119 <test> |
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120 <param name="input" value="test_in/sample.gd_snp" ftype="gd_snp" /> |
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121 <param name="choice" value="0" /> |
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122 <param name="minimum_coverage" value="3" /> |
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123 <param name="minimum_quality" value="30" /> |
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124 <param name="data_source" value="0" /> |
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125 <param name="branch_style" value="" /> |
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126 <param name="scale_style" value="" /> |
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127 <param name="length_style" value="" /> |
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128 <param name="layout_style" value="" /> |
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129 <output name="output" file="test_out/phylogenetic_tree/phylogenetic_tree.html" ftype="html" compare="diff" lines_diff="2"> |
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130 <extra_files type="file" name="distance_matrix.phylip" value="test_out/phylogenetic_tree/distance_matrix.phylip" /> |
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131 <extra_files type="file" name="informative_snps.txt" value="test_out/phylogenetic_tree/informative_snps.txt" /> |
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132 <extra_files type="file" name="mega_distance_matrix.txt" value="test_out/phylogenetic_tree/mega_distance_matrix.txt" /> |
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133 <extra_files type="file" name="phylogenetic_tree.newick" value="test_out/phylogenetic_tree/phylogenetic_tree.newick" /> |
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134 <extra_files type="file" name="tree.pdf" value="test_out/phylogenetic_tree/tree.pdf" compare="sim_size" delta = "1000"/> |
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135 </output> |
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136 </test> |
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137 </tests> |
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138 |
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139 <requirements> |
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140 <requirement type="package" version="1.3">phast</requirement> |
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141 <requirement type="package" version="1.1">quicktree</requirement> |
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142 <requirement type="package" version="0.1">gd_c_tools</requirement> |
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143 </requirements> |
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144 |
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145 |
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146 <help> |
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147 |
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148 **Dataset formats** |
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149 |
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150 The input dataset is in gd_snp_ or gd_genotype_ format. |
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151 The output is a composite dataset, containing the tree in both text (Newick_) |
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152 and PostScript formats, as well as supplemental text information. |
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153 (`Dataset missing?`_) |
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154 |
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155 .. _gd_snp: ./static/formatHelp.html#gd_snp |
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156 .. _gd_genotype: ./static/formatHelp.html#gd_genotype |
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157 .. _Newick: http://evolution.genetics.washington.edu/phylip/newicktree.html |
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158 .. _Dataset missing?: ./static/formatHelp.html |
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159 |
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160 ----- |
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161 |
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162 **What it does** |
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163 |
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164 This tool uses a gd_snp dataset to determine a kind of "genetic distance" |
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165 between each pair of individuals. That information is used to |
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166 produce a tree-shaped figure that depicts how the individuals are related, |
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167 both as a text files and as a diagram. |
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168 The text files include a common tree format, Newick, as well as distance |
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169 matrices and counts of informative SNPs for each pairwise comparison. |
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170 The informative SNPs can be used as a guide to how reliable the tree is. |
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171 |
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172 The input parameters are: |
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173 |
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174 SNP dataset |
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175 A table of SNPs for various individuals, in gd_snp format. |
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176 |
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177 Individuals |
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178 By default all individuals are included in the analysis, but this can |
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179 optionally be restricted to a subset that has been defined using the |
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180 Specify Individuals tool. |
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181 |
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182 Minimum SNP coverage |
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183 For each pair of individuals, the tool looks for informative SNPs, i.e., |
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184 where the sequence data for both individuals is adequate. Specifying, |
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185 say, 7 for this option instructs the tool to consider only SNPs with |
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186 at least 7 reads in each of the two individuals (regardless of the |
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187 alleles) when estimating their genetic distance. |
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188 |
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189 Minimum SNP quality |
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190 Specifying, say, 37 for this option instructs the tool to consider |
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191 only SNPs with a quality score of at least 37 in both individuals |
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192 when estimating their genetic distance. |
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193 |
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194 Include reference sequence |
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195 For gd_snp datasets containing columns for a reference sequence, the |
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196 user can ask that the reference be indicated in the tree, to help with |
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197 rooting it. If the dataset has no reference columns, this option has |
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198 no effect. |
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199 |
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200 Distance metric |
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201 The genetic distance between two individuals at a given SNP can |
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202 be estimated two ways. One method is to use the absolute value of the |
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203 difference in the frequency of the first allele (or equivalently, the |
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204 second allele). For instance, if the first individual has 5 reads of |
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205 each allele and the second individual has respectively 3 and 6 reads, |
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206 then the frequencies are 1/2 and 1/3, giving a distance 1/6 at that |
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207 SNP. The other approach is to use the genotype calls to estimate |
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208 the difference in the number of occurrences of the first allele. |
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209 For instance, if the two genotypes are 2 and 1, i.e., the individuals |
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210 are estimated to have respectively 2 and 1 occurrences of the first |
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211 allele at this location, then the distance is 1 (the absolute value |
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212 of the difference of the two numbers). |
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213 |
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214 Output options |
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215 The final four options apply mostly to the graphical drawing of the |
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216 tree, except that the branch lengths are also added to the Newick text |
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217 file. |
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218 |
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219 ----- |
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220 |
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221 **Acknowledgments** |
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222 |
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223 To convert the distance matrix to a Newick-formatted tree, we use the |
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224 QuickTree program from |
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225 http://www.sanger.ac.uk/resources/software/quicktree/ . |
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226 |
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227 To make the diagram we use draw_tree, available at |
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228 http://compgen.bscb.cornell.edu/phast/ . |
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229 |
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230 </help> |
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231 </tool> |