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annotate add_fst_column.xml @ 28:184d14e4270d

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Update to Miller Lab devshed revision 4ede22dd5500
author Richard Burhans <burhans@bx.psu.edu>
date Wed, 17 Jul 2013 12:46:46 -0400
parents 8997f2ca8c7a
children a631c2f6d913
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1 <tool id="gd_add_fst_column" name="Per-SNP FSTs" version="1.2.0">
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2 <description>: Compute a fixation index score for each SNP</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 add_fst_column.py '$input' '$p1_input' '$p2_input'
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15 #if $input_type.choice == '0'
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16 'gd_snp' '$input_type.data_source.choice'
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17 #if $input_type.data_source.choice == '0'
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18 '$input_type.data_source.min_reads' '$input_type.data_source.min_qual'
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19 #else if $input_type.data_source.choice == '1'
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20 '0' '0'
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21 #end if
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22 #else if $input_type.choice == '1'
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23 'gd_genotype' '1' '0' '0'
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24 #end if
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25 '$retain' '$discard_fixed' '$biased' '$output' '$ind_arg'
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26 </command>
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28 <inputs>
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29 <conditional name="input_type">
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30 <param name="choice" type="select" format="integer" label="Input format">
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31 <option value="0" selected="true">gd_snp</option>
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32 <option value="1">gd_genotype</option>
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33 </param>
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34
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35 <when value="0">
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36 <param name="input" type="data" format="gd_snp" label="SNP dataset" />
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37
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38 <conditional name="data_source">
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39 <param name="choice" type="select" format="integer" label="Frequency metric">
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40 <option value="0">sequence coverage</option>
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41 <option value="1" selected="true">estimated genotype</option>
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42 </param>
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43 <when value="0">
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44 <param name="min_reads" type="integer" min="0" value="0" label="Minimum total read count for a population" />
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45 <param name="min_qual" type="integer" min="0" value="0" label="Minimum individual genotype quality" />
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46 </when>
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47 <when value="1"/>
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48 </conditional>
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49 </when>
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50 <when value="1">
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51 <param name="input" type="data" format="gd_genotype" label="Genotype dataset" />
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52 </when>
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53 </conditional>
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54
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55 <param name="p1_input" type="data" format="gd_indivs" label="Population 1 individuals" />
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56 <param name="p2_input" type="data" format="gd_indivs" label="Population 2 individuals" />
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57
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58 <param name="retain" type="select" label="If a SNP is below minimum">
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59 <option value="0" selected="true">skip SNP</option>
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60 <option value="1">set FST = -1</option>
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61 </param>
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62
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63 <param name="discard_fixed" type="select" label="For SNPs that appear to be fixed across both populations">
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64 <option value="0">retain</option>
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65 <option value="1" selected="true">delete</option>
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66 </param>
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67
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68 <param name="biased" type="select" label="FST estimator">
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69 <option value="0">Wright's original definition</option>
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70 <option value="1">the Weir-Cockerham estimator</option>
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71 <option value="2" selected="true">the Reich-Patterson estimator</option>
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72 </param>
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73
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74 </inputs>
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75
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76 <outputs>
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77 <data name="output" format="input" format_source="input" metadata_source="input" />
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78 </outputs>
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79
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80 <tests>
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81 <test>
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82 <param name="input" value="test_in/sample.gd_snp" ftype="gd_snp" />
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83 <param name="p1_input" value="test_in/a.gd_indivs" ftype="gd_indivs" />
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84 <param name="p2_input" value="test_in/b.gd_indivs" ftype="gd_indivs" />
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85 <param name="data_source" value="0" />
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86 <param name="min_reads" value="3" />
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87 <param name="min_qual" value="0" />
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88 <param name="retain" value="0" />
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89 <param name="discard_fixed" value="1" />
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90 <param name="biased" value="0" />
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91 <output name="output" file="test_out/add_fst_column/add_fst_column.gd_snp" />
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92 </test>
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93 </tests>
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94
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95 <help>
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96
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97 **Dataset formats**
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98
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99 The input datasets are in gd_snp_, gd_genotype_, and gd_indivs_ formats.
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100 The output dataset is in gd_snp_ or gd_genotype_ format. (`Dataset missing?`_)
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101
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102 .. _gd_snp: ./static/formatHelp.html#gd_snp
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103 .. _gd_genotype: ./static/formatHelp.html#gd_genotype
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104 .. _gd_indivs: ./static/formatHelp.html#gd_indivs
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105 .. _Dataset missing?: ./static/formatHelp.html
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106
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107 -----
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108
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109 **What it does**
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110
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111 The user specifies a SNP table and two "populations" of individuals, both previously defined using the Galaxy tool to specify individuals from a SNP table. No individual can be in both populations. Other choices are as follows.
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112
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113 Frequency metric. The allele frequencies of a SNP in the two populations can be estimated either by the total number of reads of each allele (if the table is in gd_snp format, but not with gd_genotype), or by adding the frequencies inferred from genotypes of individuals in the populations.
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114
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115 After specifying the frequency metric, the user sets lower bounds on amount of data required at a SNP. For estimating the Fst using read counts, the bound is the minimum count of reads of the two alleles in a population. For estimations based on genotype, the bound is the minimum reported genotype quality per individual.
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116
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117 The user specifies whether the SNPs that violate the lower bound should be ignored or the Fst set to -1.
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118
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119 The user specifies whether SNPs where both populations appear to be fixed for the same allele should be retained or discarded.
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120
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121 Finally, the user chooses which definition of Fst to use: Wright's original definition, the Weir-Cockerham unbiased estimator, or the Reich-Patterson estimator.
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122
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123 A column is appended to the SNP table giving the Fst for each retained SNP.
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124
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125 References:
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126
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127 Sewall Wright (1951) The genetical structure of populations. Ann Eugen 15:323-354.
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128
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129 Weir, B.S. and Cockerham, C. Clark (1984) Estimating F-statistics for the analysis of population structure. Evolution 38:1358-1370.
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130
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131 Weir, B.S. 1996. Population substructure. Genetic data analysis II, pp. 161-173. Sinauer Associates, Sundand, MA.
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132
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133 David Reich, Kumarasamy Thangaraj, Nick Patterson, Alkes L. Price, and Lalji Singh (2009) Reconstructing Indian population history. Nature 461:489-494, especially Supplement 2.
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134
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135 Their effectiveness for computing FSTs when there are many SNPs but few individuals is discussed in the following paper.
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136
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137 Eva-Maria Willing, Christine Dreyer, Cock van Oosterhout (2012) Estimates of genetic differentiation measured by FST do not necessarily require large sample sizes when using many SNP markers. PLoS One 7:e42649.
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138
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139 -----
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140
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141 **Example**
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142
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143 - input, SNP table::
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144
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145 #{"column_names":["scaf","pos","A","B","qual","ref","rpos","rnuc","1A","1B","1G","1Q","2A","2B","2G","2Q","3A","3B","3G","3Q","4A","4B","4G","4Q",
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146 #"5A","5B","5G","5Q","6A","6B","6G","6Q","pair","dist","prim","rflp"],"dbkey":"canFam2",
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147 #"individuals":[["PB1",9],["PB2",13],["PB3",17],["PB4",21],["PB6",25],["PB8",29]],
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148 #"pos":2,"rPos":7,"ref":6,"scaffold":1,"species":"bear"}
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149 Contig161_chr1_4641264_4641879 115 C T 73.5 chr1 4641382 C 6 0 2 45 8 0 2 51 15 0 2 72 5 0 2 42 6 0 2 45 10 0 2 57 Y 54 0.323 0
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150 Contig113_chr5_11052263_11052603 28 C T 38.2 chr5 11052280 C 1 2 1 12 3 2 1 10 5 0 2 42 2 1 2 13 3 0 2 36 8 0 2 51 Y 161 +99. 0
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151 Contig215_chr5_70946445_70947428 363 T G 28.2 chr5 70946809 C 4 0 2 39 0 5 0 12 9 0 2 54 6 0 2 45 3 3 2 1 9 0 2 54 N 43 0.153 0
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152 etc.
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153
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154 - input, Population 1 individuals::
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155
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156 9 PB1
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157 13 PB2
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158
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159 - input, Population 2 individuals::
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160
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161 17 PB3
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162 21 PB4
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163
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164 - output (minimum read count of 3, discard fixed)::
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165
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166 Contig113_chr5_11052263_11052603 28 C T 38.2 chr5 11052280 C 1 2 1 12 3 2 1 10 5 0 2 42 2 1 2 13 3 0 2 36 8 0 2 51 Y 161 +99. 0 0.1636
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167 Contig215_chr5_70946445_70947428 363 T G 28.2 chr5 70946809 C 4 0 2 39 0 5 0 12 9 0 2 54 6 0 2 45 3 3 2 1 9 0 2 54 N 43 0.153 0 0.3846
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168 etc.
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169
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170 </help>
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171 </tool>