Mercurial > repos > iuc > varscan_somatic

annotate varscan_somatic.xml @ 7:2657ab48e16a draft

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planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit f5e4d8903b6d69b0507f6a8fc4c2533fc7a15dfa
author iuc
date Mon, 21 Jan 2019 12:05:00 -0500
parents 2c66c4025db2
children b79bb8b09822
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1 <tool id="varscan_somatic" name="VarScan somatic" version="@VERSION@.3">
2
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2 <description>Call germline/somatic and LOH variants from tumor-normal sample pairs</description>
0
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3 <macros>
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4 <import>macros.xml</import>
2
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5 <macro name="test_mentions_contig">
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6 <assert_contents>
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7 <has_line_matching
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8 expression="##contig=.ID=chrM,length=16571." />
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9 </assert_contents>
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10 </macro>
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11 <macro name="test_mentions_filters">
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12 <assert_contents>
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13 <has_line_matching
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14 expression="##FILTER=.ID=VarCount,Description=.+" />
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15 <has_line_matching
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16 expression="##FILTER=.ID=ReadLenDiff,Description=.+" />
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17 <has_line_matching
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18 expression="##FILTER=.ID=RefDist3,Description=.+" />
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19 </assert_contents>
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20 </macro>
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21 <macro name="test_not_mentions_filters">
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22 <assert_contents>
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23 <not_has_text
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24 text="##FILTER=&lt;ID=VarCount,Description=" />
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25 <not_has_text
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26 text="##FILTER=&lt;ID=ReadLenDiff,Description=" />
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27 <not_has_text
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28 text="##FILTER=&lt;ID=RefDist3,Description=" />
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29 </assert_contents>
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30 </macro>
0
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31 </macros>
2
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32 <expand macro="requirements">
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33 <requirement type="package" version="3.6.7">python</requirement>
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34 <requirement type="package" version="0.15.1">pysam</requirement>
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35 </expand>
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36 <stdio>
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37 <exit_code range="1:" />
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38 </stdio>
0
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39 <command><![CDATA[
2
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40 #if str($reference.source) == "history":
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41 #set $ref_genome = 'ref.fa'
2
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42 ln -s -f '$reference.genome' $ref_genome &&
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43 #else:
5
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44 #set $ref_genome = str($reference.genome.fields.path)
2
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45 #end if
5
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46 #set $normal_data = 'normal.bam'
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47 #set $tumor_data = 'tumor.bam'
2
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48 ln -s -f '$normal_bam' $normal_data &&
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49 ln -s -f '$tumor_bam' $tumor_data &&
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50 ln -s -f '${normal_bam.metadata.bam_index}' ${normal_data}.bai &&
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51 ln -s -f '${tumor_bam.metadata.bam_index}' ${tumor_data}.bai &&
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52 python3 $__tool_directory__/varscan.py
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53 --normal '$normal_data'
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54 --tumor '$tumor_data'
0
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55 --normal-purity ${normal_purity}
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56 --tumor-purity ${tumor_purity}
2
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57 #if str($split_output):
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58 --ofile variants_out
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59 $split_output
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60 #else:
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61 --ofile '$output'
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62 #end if
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63 --threads \${GALAXY_SLOTS:-2}
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64 #if str($call_params.settings) == "custom":
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65 ## samtools mpileup parameters
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66 --min-basequal ${call_params.min_avg_qual}
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67 --min-mapqual ${call_params.min_mapqual}
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68 ## VarScan parameters
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69 --min-coverage ${call_params.min_coverage}
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70 --min-var-count ${call_params.min_reads2}
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71 --min-var-freq ${call_params.min_var_freq}
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72 --min-hom-freq ${call_params.min_freq_for_hom}
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73 --p-value ${call_params.p_value}
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74 --somatic-p-value ${call_params.somatic_p_value}
0
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75 #end if
2
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76 #if str($filter_params.settings) == "no_filter":
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77 --no-filters
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78 #elif str($filter_params.settings) == "dream3_settings":
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79 --min-var-count2 3
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80 --min-var-count2-lc 1
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81 --min-var-freq2 0.05
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82 --max-somatic-p 0.05
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83 --max-somatic-p-depth 10
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84 --min-ref-readpos 0.2
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85 --min-var-readpos 0.15
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86 --min-ref-dist3 0.2
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87 --min-var-dist3 0.15
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88 --min-ref-len 90
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89 --min-var-len 90
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90 --max-len-diff 0.05
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91 --min-strandedness 0
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92 --min-strand-reads 5
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93 --min-ref-basequal 15
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94 --min-var-basequal 30
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95 --max-basequal-diff 50
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96 --min-ref-mapqual 20
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97 --min-var-mapqual 30
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98 --max-mapqual-diff 10
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99 --max-ref-mmqs 50
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100 --max-var-mmqs 100
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101 --min-mmqs-diff 0
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102 --max-mmqs-diff 50
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103 #elif str($filter_params.settings) == "custom":
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104 --min-var-count2 ${filter_params.min_var_count}
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105 --min-var-count2-lc ${filter_params.min_var_count_lc}
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106 --min-var-freq2 ${filter_params.min_var_freq2}
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107 --max-somatic-p ${filter_params.max_somatic_p}
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108 --max-somatic-p-depth ${filter_params.max_somatic_p_depth}
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109 --min-ref-readpos ${filter_params.min_ref_readpos}
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110 --min-var-readpos ${filter_params.min_var_readpos}
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111 --min-ref-dist3 ${filter_params.min_ref_dist3}
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112 --min-var-dist3 ${filter_params.min_var_dist3}
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113 --min-ref-len ${filter_params.min_ref_len}
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114 --min-var-len ${filter_params.min_var_len}
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115 --max-len-diff ${filter_params.max_len_diff}
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116 --min-strandedness ${filter_params.min_strandedness}
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117 --min-strand-reads ${filter_params.min_strand_reads}
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118 --min-ref-basequal ${filter_params.min_ref_basequal}
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119 --min-var-basequal ${filter_params.min_var_basequal}
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120 --max-basequal-diff ${filter_params.max_basequal_diff}
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121 --min-ref-mapqual ${filter_params.min_ref_mapqual}
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122 --min-var-mapqual ${filter_params.min_var_mapqual}
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123 --max-mapqual-diff ${filter_params.max_mapqual_diff}
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124 --max-ref-mmqs ${filter_params.max_ref_mmqs}
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125 --max-var-mmqs ${filter_params.max_var_mmqs}
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126 --min-mmqs-diff ${filter_params.min_mmqs_diff}
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127 --max-mmqs-diff ${filter_params.max_mmqs_diff}
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128 #end if
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129 --verbose
5
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130 '$ref_genome'
0
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131 ]]></command>
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132
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133 <inputs>
2
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134 <conditional name="reference">
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135 <param name="source" type="select"
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136 label="Will you select a reference genome from your history or use a built-in genome?">
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137 <option value="cached">Use a built-in genome</option>
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138 <option value="history">Use a genome from my history</option>
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139 </param>
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140 <when value="cached">
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141 <param name="genome" type="select"
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142 label="reference genome"
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143 help="The fasta reference genome that variants should be called against.">
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144 <options from_data_table="fasta_indexes" />
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145 </param>
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146 </when>
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147 <when value="history">
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148 <param name="genome" type="data" format="fasta"
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149 label="reference genome"
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150 help="The fasta reference genome that variants should be called against."/>
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151 </when>
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152 </conditional>
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153 <param name="normal_bam" type="data" format="bam"
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154 label="aligned reads from normal sample" />
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155 <param name="tumor_bam" type="data" format="bam"
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156 label="aligned reads from tumor sample" />
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157 <param argument="--normal-purity" name="normal_purity" type="float" value="1.0" min="0" max="1.0"
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158 label="Estimated purity (non-tumor content) of normal sample"/>
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159 <param argument="--tumor-purity" name="tumor_purity" type="float" value="1.0" min="0" max="1.0"
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160 label="Estimated purity (tumor content) of tumor sample"/>
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161 <param name="split_output" type="boolean" truevalue="--split-output" falsevalue="" checked="false"
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162 label="Generate separate output datasets for SNP and indel calls?" />
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163 <conditional name="call_params">
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164 <param name="settings" label="Settings for Variant Calling" type="select">
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165 <option value="varscan_defaults" selected="true">Use default values</option>
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166 <option value="custom">Customize settings</option>
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167 </param>
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168 <when value="custom">
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169 <param argument="samtools mpileup -Q" name="min_avg_qual" type="integer" value="13" min="0" max="50"
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170 label="Minimum base quality"
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171 help="The minimum base quality at the variant position required to use a read for calling" />
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172 <param argument="samtools mpileup -q" name="min_mapqual" type="integer" value="0" min="0" max="60"
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173 label="Minimum mapping quality"
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174 help="The minimum mapping quality required for a read to be considered in variant calling" />
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175 <expand macro="min_coverage"
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176 help="Minimum site coverage required in the normal and in the tumor sample to call a variant. This threshold gets applied after eliminating reads with low base and mapping qualitiy as defined above." />
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177 <expand macro="min_reads2" />
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178 <expand macro="min_var_freq" value="0.1" />
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179 <expand macro="min_freq_for_hom" />
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180 <expand macro="p_value" value="0.99"
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181 help="The p-value threshold used to determine if a variant should be called for either sample" />
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182 <param argument="--somatic-p-value" name="somatic_p_value" type="float" value="0.05" min="0" max="1"
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
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183 label="P-value threshold for calling somatic variants and LOH events"
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184 help="The p-value threshold used to determine if read count differences between the normal and the tumor sample justify classification of a variant as somatic or as an LOH event" />
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185 </when>
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186 <when value="varscan_defaults" />
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187 </conditional>
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188 <conditional name="filter_params">
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189 <param name="settings" label="Settings for Posterior Variant Filtering" type="select">
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190 <option value="varscan_defaults" selected="true">Use default values</option>
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191 <option value="dream3_settings">Use settings optimized for DREAM-3</option>
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192 <option value="no_filter">Do not perform posterior filtering</option>
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193 <option value="custom">Customize settings</option>
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194 </param>
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195 <when value="varscan_defaults" />
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196 <when value="dream3_settings" />
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197 <when value="no_filter" />
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198 <when value="custom">
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199 <param argument="--min-var-count" name="min_var_count" type="integer" value="4" min="1" max="200"
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200 label="Minimum number of variant-supporting reads"
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201 help="" />
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202 <param argument="--min-var-count-lc" name="min_var_count_lc" type="integer" value="2" min="1" max="200"
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
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203 label="Low coverage minimum number of variant-supporting reads"
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204 help="Will be applied instead of the --min-var-count limit for sites with poor overall (less than --max-somatic-p-depth) coverage" />
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205 <param argument="--min-var-freq" name="min_var_freq2" type="float" value="0.05" min="0" max="1"
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
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206 label="Minimum variant allele frequency"
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207 help="" />
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208 <param argument="--max-somatic-p" name="max_somatic_p" type="float" value="0.05" min="0" max="1"
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
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209 label="Maximum somatic p-value allowed for a somatic call"
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210 help="" />
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
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211 <param argument="--max-somatic-p-depth" name="max_somatic_p_depth" type="integer" value="10" min="2" max="200"
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
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212 label="Depth required at variant site to run --max-somatic-p filter"
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213 help="" />
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214 <param argument="--min-ref-readpos" name="min_ref_readpos" type="float" value="0.1" min="0" max="1"
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
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215 label="Minimum relative variant position in ref-supporting reads"
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216 help="The minimum average relative distance from the ends of ref-supporting reads required for variant sites" />
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
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217 <param argument="--min-var-readpos" name="min_var_readpos" type="float" value="0.1" min="0" max="1"
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
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218 label="Minimum relative variant position in variant-supporting reads"
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219 help="The minimum average relative distance from the ends of variant-supporting reads required for variant sites" />
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
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220 <param argument="--min-ref-dist3" name="min_ref_dist3" type="float" value="0.1" min="0" max="1"
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
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221 label="Minimum distance of variant site from 3'-end of ref-supporting reads"
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
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222 help="The minimum average relative distance from the effective 3'end of ref-supporting reads required for variant sites" />
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
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223 <param argument="--min-var-dist3" name="min_var_dist3" type="float" value="0.1" min="0" max="1"
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
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224 label="Minimum distance of variant site from 3'-end of variant-supporting reads"
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
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225 help="The minimum average relative distance from the effective 3'end of variant-supporting reads required for variant sites" />
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
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226 <param argument="--min-ref-avgrl" name="min_ref_len" type="integer" value="90" min="0" max="200"
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
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227 label="Minimum length of ref-supporting reads"
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228 help="The minimum average trimmed length required for reads supporting the reference allele" />
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
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229 <param argument="--min-var-avgrl" name="min_var_len" type="integer" value="90" min="0" max="200"
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
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230 label="Minimum length of variant-supporting reads"
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231 help="The minimum average trimmed length required for reads supporting the variant allele" />
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232 <param argument="--max-rl-diff" name="max_len_diff" type="float" value="0.25" min="0" max="1"
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
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233 label="Maximum relative read length difference"
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234 help="The maximum allowed average relative read length difference (ref - var) between reads supporting the reference and the variant allele" />
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
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235 <param argument="--min-strandedness" name="min_strandedness" type="float" value="0.01" min="0" max="0.5"
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
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236 label="Minimum fraction of variant reads from each strand"
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237 help="The minimum fraction of variant reads that are required to come from the forward and from the reverse strand" />
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
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238 <param argument="--min-strand-reads" name="min_strand_reads" type="integer" value="5" min="2" max="200"
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
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239 label="Minimum variant allele depth required to apply the --min-strandedness filter"
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240 help="" />
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241 <param argument="--min-ref-basequal" name="min_ref_basequal" type="integer" value="15" min="1" max="50"
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
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242 label="Minimum average base quality for the ref allele"
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243 help="The minimum average base quality required at the variant site for reads supporting the reference allele" />
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
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244 <param argument="--min-var-basequal" name="min_var_basequal" type="integer" value="15" min="1" max="50"
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
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245 label="Minimum average base quality for the variant allele"
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
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246 help="The minimum average base quality required at the variant site for reads supporting the variant allele" />
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247 <param argument="max-basequal-diff" name="max_basequal_diff" type="integer" value="50" min="0" max="50"
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
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248 label="Maximum base quality difference between ref- and variant-supporting reads"
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
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249 help="The maximum average base quality difference (ref - var) allowed between the variant site positions of reads supporting the reference and the variant allele" />
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
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250 <param argument="--min-ref-mapqual" name="min_ref_mapqual" type="integer" value="15" min="1" max="60"
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
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251 label="Minimum average mapping quality of ref-supporting reads"
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
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252 help="The minimum average mapping quality required for reads supporting the reference allele" />
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
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253 <param argument="--min-var-mapqual" name="min_var_mapqual" type="integer" value="15" min="1" max="60"
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
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254 label="Minimum average mapping quality of variant-supporting reads"
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255 help="The minimum average mapping quality required for reads supporting the variant allele" />
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256 <param argument="--max-mapqual-diff" name="max_mapqual_diff" type="integer" value="50" min="0" max="60"
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
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257 label="Maximum mapping quality difference between ref- and variant-supporting reads"
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258 help="The maximum average mapping quality difference (ref - var) allowed between reads supporting the reference and the variant allele" />
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259 <param argument="--max-ref-mmqs" name="max_ref_mmqs" type="integer" value="100" min="0"
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260 label="Maximum mismatch base quality sum of ref-supporting reads"
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261 help="The maximum mismatch base quality sum allowed for reads supporting the reference allele" />
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262 <param argument="--max-var-mmqs" name="max_var_mmqs" type="integer" value="100" min="0"
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263 label="Maximum mismatch base quality sum of var-supporting reads"
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264 help="The maximum mismatch base quality sum allowed for reads supporting the variant allele" />
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265 <param argument="--min-mmqs-diff" name="min_mmqs_diff" type="integer" value="0" min="0"
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266 label="Minimum difference between mismatch base quality sums of variant- and ref-supporting reads"
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267 help="The minimum difference in the mismatch base quality sums (var - ref) required between reads supporting the variant and the reference allele" />
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
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268 <param argument="--max-mmqs-diff" name="max_mmqs_diff" type="integer" value="50" min="1"
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269 label="Maximum difference between mismatch base quality sums of variant- and ref-supporting reads"
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270 help="The maximum difference in the mismatch base quality sums (var - ref) allowed between reads supporting the variant and the reference allele" />
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271 </when>
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272 </conditional>
0
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273 </inputs>
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274 <outputs>
2
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275 <data name="output" format="vcf">
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276 <filter>not split_output</filter>
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277 </data>
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278 <data name="output_snp" from_work_dir="variants_out.snp" format="vcf"
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279 label="Varscan somatic SNP calls on ${on_string}">
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280 <filter>split_output</filter>
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281 </data>
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282 <data name="output_indel" from_work_dir="variants_out.indel" format="vcf"
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283 label="Varscan somatic indel calls on ${on_string}">
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284 <filter>split_output</filter>
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285 </data>
0
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286 </outputs>
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287 <tests>
2
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288 <test expect_num_outputs="1">
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289 <conditional name="reference">
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290 <param name="source" value="history" />
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291 <param name="genome" value="hg19_chrM.fa" />
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292 </conditional>
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293 <param name="normal_bam" value="control_chrM.bam" />
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
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294 <param name="tumor_bam" value="tumor_chrM.bam" />
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295 <param name="split_output" value="false" />
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296 <conditional name="call_params">
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297 <param name="settings" value="varscan_defaults" />
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298 </conditional>
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299 <conditional name="filter_params">
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300 <param name="settings" value="varscan_defaults" />
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301 </conditional>
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302 <output name="output">
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303 <expand macro="test_mentions_contig" />
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304 <expand macro="test_mentions_filters" />
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305 </output>
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306 </test>
5
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parents: 2
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307 <test expect_num_outputs="1">
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308 <conditional name="reference">
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309 <param name="source" value="cached" />
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310 <param name="genome" value="hg19mito" />
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311 </conditional>
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312 <param name="normal_bam" dbkey="hg19" value="control_chrM.bam" />
d37adcc2ec03 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3a2e62daa15beefe2015ed68cc862b88ade31934
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313 <param name="tumor_bam" dbkey="hg19" value="tumor_chrM.bam" />
d37adcc2ec03 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3a2e62daa15beefe2015ed68cc862b88ade31934
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314 <param name="split_output" value="false" />
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315 <conditional name="call_params">
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316 <param name="settings" value="varscan_defaults" />
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317 </conditional>
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318 <conditional name="filter_params">
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319 <param name="settings" value="varscan_defaults" />
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320 </conditional>
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321 <output name="output">
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322 <expand macro="test_mentions_contig" />
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323 <expand macro="test_mentions_filters" />
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324 </output>
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325 </test>
2
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326 <test expect_num_outputs="2">
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327 <conditional name="reference">
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328 <param name="source" value="history" />
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
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parents: 1
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329 <param name="genome" value="hg19_chrM.fa" />
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
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330 </conditional>
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331 <param name="normal_bam" value="control_chrM.bam" />
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
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332 <param name="tumor_bam" value="tumor_chrM.bam" />
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333 <param name="split_output" value="true" />
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334 <conditional name="call_params">
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335 <param name="settings" value="varscan_defaults" />
1
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parents: 0
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336 </conditional>
2
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parents: 1
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337 <conditional name="filter_params">
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338 <param name="settings" value="varscan_defaults" />
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339 </conditional>
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340 <output name="output_indel">
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341 <expand macro="test_mentions_contig" />
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342 <expand macro="test_mentions_filters" />
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343 </output>
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344 <output name="output_snp">
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345 <expand macro="test_mentions_contig" />
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diff changeset
346 <expand macro="test_mentions_filters" />
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diff changeset
347 </output>
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents: 1
diff changeset
348 </test>
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents: 1
diff changeset
349 <test expect_num_outputs="1">
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents: 1
diff changeset
350 <conditional name="reference">
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents: 1
diff changeset
351 <param name="source" value="history" />
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents: 1
diff changeset
352 <param name="genome" value="hg19_chrM.fa" />
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents: 1
diff changeset
353 </conditional>
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents: 1
diff changeset
354 <param name="normal_bam" value="control_chrM.bam" />
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents: 1
diff changeset
355 <param name="tumor_bam" value="tumor_chrM.bam" />
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents: 1
diff changeset
356 <param name="split_output" value="false" />
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents: 1
diff changeset
357 <conditional name="call_params">
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents: 1
diff changeset
358 <param name="settings" value="custom" />
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents: 1
diff changeset
359 <param name="min_coverage" value="2" />
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents: 1
diff changeset
360 <param name="min_reads2" value="1" />
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents: 1
diff changeset
361 <param name="min_avg_qual" value="5" />
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents: 1
diff changeset
362 <param name="min_var_freq" value="0.01" />
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents: 1
diff changeset
363 <param name="min_freq_for_hom" value="0.66" />
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents: 1
diff changeset
364 <param name="p_value" value="0.97" />
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents: 1
diff changeset
365 <param name="somatic_p_value" value="0.09" />
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents: 1
diff changeset
366 </conditional>
0
72b8ce355fae planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
iuc
parents:
diff changeset
367 <param name="normal_purity" value="0.6" />
72b8ce355fae planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
iuc
parents:
diff changeset
368 <param name="tumor_purity" value="0.6" />
2
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents: 1
diff changeset
369 <conditional name="filter_params">
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents: 1
diff changeset
370 <param name="settings" value="varscan_defaults" />
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents: 1
diff changeset
371 </conditional>
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents: 1
diff changeset
372 <assert_stderr>
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents: 1
diff changeset
373 <has_line_matching
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents: 1
diff changeset
374 expression=" Min coverage:&#09;2x for Normal, 2x for Tumor" />
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents: 1
diff changeset
375 <has_line_matching
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents: 1
diff changeset
376 expression="Min reads2:&#09;1" />
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents: 1
diff changeset
377 <has_line_matching
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents: 1
diff changeset
378 expression="Min var freq:&#09;0.01" />
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents: 1
diff changeset
379 <has_line_matching
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents: 1
diff changeset
380 expression="Min freq for hom:&#09;0.66" />
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents: 1
diff changeset
381 <has_line_matching
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents: 1
diff changeset
382 expression="Normal purity:&#09;0.6" />
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents: 1
diff changeset
383 <has_line_matching
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents: 1
diff changeset
384 expression="Tumor purity:&#09;0.6" />
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents: 1
diff changeset
385 <has_line_matching
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents: 1
diff changeset
386 expression="Min avg qual:&#09;5" />
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents: 1
diff changeset
387 <has_line_matching
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents: 1
diff changeset
388 expression="P-value thresh:&#09;0.97" />
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents: 1
diff changeset
389 <has_line_matching
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents: 1
diff changeset
390 expression="Somatic p-value:&#09;0.09" />
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents: 1
diff changeset
391 </assert_stderr>
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents: 1
diff changeset
392 <output name="output">
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents: 1
diff changeset
393 <expand macro="test_mentions_contig" />
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents: 1
diff changeset
394 <expand macro="test_mentions_filters" />
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents: 1
diff changeset
395 </output>
0
72b8ce355fae planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
iuc
parents:
diff changeset
396 </test>
2
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents: 1
diff changeset
397 <test expect_num_outputs="1">
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents: 1
diff changeset
398 <conditional name="reference">
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents: 1
diff changeset
399 <param name="source" value="history" />
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents: 1
diff changeset
400 <param name="genome" value="hg19_chrM.fa" />
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents: 1
diff changeset
401 </conditional>
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents: 1
diff changeset
402 <param name="normal_bam" value="control_chrM.bam" />
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents: 1
diff changeset
403 <param name="tumor_bam" value="tumor_chrM.bam" />
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents: 1
diff changeset
404 <param name="split_output" value="false" />
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents: 1
diff changeset
405 <conditional name="call_params">
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents: 1
diff changeset
406 <param name="settings" value="varscan_defaults" />
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents: 1
diff changeset
407 </conditional>
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents: 1
diff changeset
408 <conditional name="filter_params">
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents: 1
diff changeset
409 <param name="settings" value="dream3_settings" />
1
31a38ce7e8ae planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 33c5694cb2e0a86a76d12a3355a2bd26deba7177
iuc
parents: 0
diff changeset
410 </conditional>
2
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents: 1
diff changeset
411 <output name="output">
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents: 1
diff changeset
412 <expand macro="test_mentions_contig" />
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents: 1
diff changeset
413 <expand macro="test_mentions_filters" />
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents: 1
diff changeset
414 </output>
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents: 1
diff changeset
415 </test>
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents: 1
diff changeset
416 <test expect_num_outputs="1">
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents: 1
diff changeset
417 <conditional name="reference">
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents: 1
diff changeset
418 <param name="source" value="history" />
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents: 1
diff changeset
419 <param name="genome" value="hg19_chrM.fa" />
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents: 1
diff changeset
420 </conditional>
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents: 1
diff changeset
421 <param name="normal_bam" value="control_chrM.bam" />
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents: 1
diff changeset
422 <param name="tumor_bam" value="tumor_chrM.bam" />
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents: 1
diff changeset
423 <param name="split_output" value="false" />
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents: 1
diff changeset
424 <conditional name="call_params">
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents: 1
diff changeset
425 <param name="settings" value="varscan_defaults" />
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents: 1
diff changeset
426 </conditional>
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents: 1
diff changeset
427 <conditional name="filter_params">
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents: 1
diff changeset
428 <param name="settings" value="no_filter" />
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents: 1
diff changeset
429 </conditional>
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents: 1
diff changeset
430 <output name="output">
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents: 1
diff changeset
431 <expand macro="test_mentions_contig" />
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents: 1
diff changeset
432 <expand macro="test_not_mentions_filters" />
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents: 1
diff changeset
433 </output>
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents: 1
diff changeset
434 </test>
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents: 1
diff changeset
435 <test expect_num_outputs="1">
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents: 1
diff changeset
436 <conditional name="reference">
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents: 1
diff changeset
437 <param name="source" value="history" />
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438 <param name="genome" value="hg19_chrM.fa" />
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439 </conditional>
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440 <param name="normal_bam" value="control_chrM.bam" />
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441 <param name="tumor_bam" value="tumor_chrM.bam" />
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442 <param name="split_output" value="false" />
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443 <conditional name="call_params">
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444 <param name="settings" value="varscan_defaults" />
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445 </conditional>
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446 <conditional name="filter_params">
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447 <param name="settings" value="custom" />
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448 <param name="min_ref_basequal" value="28" />
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449 <param name="min_var_basequal" value="28" />
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450 </conditional>
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451 <output name="output">
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452 <expand macro="test_mentions_contig" />
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453 <expand macro="test_mentions_filters" />
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454 </output>
1
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455 </test>
0
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456 </tests>
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457
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458 <help>
2
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459 @HELP_HEADER@
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460
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461 **The Varscan Somatic tool for Galaxy**
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462
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463 This tool wraps the functionality of the ``varscan somatic`` and the
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464 ``varscan fpfilter`` command line tools.
0
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465
2
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466 .. class:: infomark
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467
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468 The wrapper aims at providing the same functionality as the
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469 ``varscan fpfilter`` tool, but implements it using ``pysam`` internally.
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470 Note that, as one limitation compared to the original ``varscan`` tool,
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471 the current version does not apply filters to indels!
0
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472
2
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473 The tool is designed to detect genetic variants in a **pair of samples**
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474 representing normal and tumor tissue from the same individual. It classifies
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475 the variants, according to their most likely origin, as **somatic** (variant is
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476 found in the tumor, but not in the normal sample, *i.e.*, is the consequence of
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477 a somatic mutation event), **germline** (variant is found in both samples =>
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478 germline mutation event) and **LOH** (variant is found in both samples, but
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479 only the tumor sample appears to be homozygous for it => loss of heterozygosity
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480 event).
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481 This classification is encoded in the variant ``INFO`` fields of the VCF output
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482 produced by the tool in the form of a status code ``SS`` (somatic status),
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483 where:
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484
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485 - ``SS=1`` signifies a likely germline variant,
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486 - ``SS=2`` a somatic variant
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487 - ``SS=3`` a LOH variant
0
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488
2
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489 In addition, ``SS=0`` indicates a possible variant, but with insufficient
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490 evidence for an, at least, heterozygous state in either individual sample, and
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491 ``SS=5`` is used for variants of unexplained origin (*e.g.*, variants found in
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492 the normal, but not in the tumor tissue sample).
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493
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494 In a second step, following variant calling, the tool can try to detect likely
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495 false-positive calls by re-inspecting the data at the variant sites more
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496 carefully and looking for signs that may indicate problems with the
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497 sequencing data or its mapping. If a called variant is deemed a possible
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498 false-positive at this step, this gets indicated in the ``FILTER`` field of the
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499 variant record in the VCF output. For high confidence variants passing all
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500 posterior (applied after variant calling) filters the value of the field will
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501 be ``PASS``, for variants failing any of the posterior filters the value will
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502 be a ``;``-separated list of the problematic filters.
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503
0
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504
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505 **Input**
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506
2
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507 The tool takes as input a reference genome (in fasta format) and a pair of
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508 aligned reads datasets (bam format).
0
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509
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510 **Output**
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511
2
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512 A VCF dataset of called variants. When asked to *Generate separate output
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513 datasets for SNP and indel calls*, the tool will behave like the
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514 ``varscan somatic`` command line tool and produce two VCF datasets - one with
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515 just the single nucleotide variants, while the other one will store
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516 insertion/deletion variants.
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diff changeset
517
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518 **Options**
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519
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520 *Estimated purity of normal sample / of tumor sample*
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521
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522 Since, in practice, it is often impossible to isolate tissue samples without
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523 contamination from surrounding tissue or from invading cells, these two fields
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524 let you indicate your estimate of the purity of the two samples (as fractions
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525 between 0 and 1, where 1 would indicate a contamination-free sample and 0.5 a
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526 sample to which the desired tissue contributes only 50%, while the other 50%
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527 consist of cells from the other tissue type).
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528
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529 *Settings for Variant Calling*
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530
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531 Settings in this section will affect the steps of variant calling and
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532 classification. You can accept VarScan's default values for the corresponding
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533 parameters or customize them according to your needs.
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534
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535 *Settings for Posterior Variant Filtering*
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536
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537 Use the parameters in this section to configure the false-positive filtering
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538 step that follows variant calling and classification. These settings will not
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539 influence the number of variants detected nor their classification, but may
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540 change the ``FILTER`` field of variant records to indicate which variants
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541 failed to pass certain filters. You can use this information with downstream
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542 tools to exclude certain variants from further analysis steps or include only
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543 high confidence variants that passed all filters (those with ``PASS`` as their
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544 ``INFO`` field value. You can accept the orignal filter defaults of the
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545 ``varscan fpfilter`` command line tool, use the settings established for the
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546 tool in the `DREAM3 challenge`_, or choose to customize the settings.
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547 Alternatively, you can also choose to skip posterior filtering entirely, in
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548 which case all variants will have their ``INFO`` field set to ``PASS``.
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549
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550 .. _DREAM3 challenge: https://www.synapse.org/#!Synapse:syn312572/wiki/58893
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551 </help>
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552 <expand macro="citations" />
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553 </tool>