Mercurial > repos > iuc > varscan_somatic

annotate varscan_somatic.xml @ 11:cf8ffc79db67 draft default tip

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"planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 1232893782204bb041dd6ed46711295cb0bfc03f"
author iuc
date Sat, 04 Dec 2021 22:23:57 +0000
parents a57606054bd7
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rev   line source
10
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1 <tool id="varscan_somatic" name="VarScan somatic" version="@VERSION@.6">
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>
9
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31 <macro name="filter_compat_options">
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32 <section name="experts_only" title="Compatibility options for experts" expanded="false">
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33 <param name="compat_opts" type="select" display="checkboxes" multiple="true" optional="true"
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34 label="Compatibility Options for Posterior Variant Filtering"
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35 help="">
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36 <option value="--ignore-md" selected="true">Always determine mismatch quality statistics from recalculated read to reference alignments. Ignore read MD tags if present.</option>
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37 <option value="--detect-q2-runs" selected="false">Treat runs of base qualities of value 2 at the 3' end of reads as quality control indicator (Illumina 1.5 compatibility setting)</option>
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38 </param>
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39 </section>
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40 </macro>
0
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41 </macros>
2
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42 <expand macro="requirements">
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43 <requirement type="package" version="3.6.7">python</requirement>
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44 <requirement type="package" version="0.15.1">pysam</requirement>
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45 </expand>
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46 <stdio>
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47 <exit_code range="1:" />
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48 </stdio>
0
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49 <command><![CDATA[
2
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50 #if str($reference.source) == "history":
5
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51 #set $ref_genome = 'ref.fa'
2
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52 ln -s -f '$reference.genome' $ref_genome &&
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53 #else:
5
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54 #set $ref_genome = str($reference.genome.fields.path)
2
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55 #end if
5
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56 #set $normal_data = 'normal.bam'
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57 #set $tumor_data = 'tumor.bam'
2
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58 ln -s -f '$normal_bam' $normal_data &&
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59 ln -s -f '$tumor_bam' $tumor_data &&
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60 ln -s -f '${normal_bam.metadata.bam_index}' ${normal_data}.bai &&
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61 ln -s -f '${tumor_bam.metadata.bam_index}' ${tumor_data}.bai &&
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62 python3 $__tool_directory__/varscan.py
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63 --normal '$normal_data'
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64 --tumor '$tumor_data'
0
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65 --normal-purity ${normal_purity}
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66 --tumor-purity ${tumor_purity}
2
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67 #if str($split_output):
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68 --ofile variants_out
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69 $split_output
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70 #else:
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71 --ofile '$output'
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72 #end if
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73 --threads \${GALAXY_SLOTS:-2}
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74 #if str($call_params.settings) == "custom":
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75 ## samtools mpileup parameters
9
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76 --min-basequal ${call_params.read_selection.min_basequal}
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77 --min-mapqual ${call_params.read_selection.min_mapqual}
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78 ${call_params.read_selection.count_orphans}
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79 ${call_params.read_selection.detect_overlaps}
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80 --max-pileup-depth ${call_params.read_selection.max_pileup_depth}
2
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81 ## VarScan parameters
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82 --min-coverage ${call_params.min_coverage}
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83 --min-var-count ${call_params.min_reads2}
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84 --min-var-freq ${call_params.min_var_freq}
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85 --min-hom-freq ${call_params.min_freq_for_hom}
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86 --p-value ${call_params.p_value}
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87 --somatic-p-value ${call_params.somatic_p_value}
0
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88 #end if
2
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89 #if str($filter_params.settings) == "no_filter":
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90 --no-filters
9
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91 #else:
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92 #if str($filter_params.settings) == "dream3_settings":
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93 --min-var-count2 3
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94 --min-var-count2-lc 1
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95 --min-var-count2-depth 10
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96 --min-var-freq2 0.05
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97 --min-ref-readpos 0.2
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98 --min-var-readpos 0.15
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99 --min-ref-dist3 0.2
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100 --min-var-dist3 0.15
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101 --min-ref-len 90
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102 --min-var-len 90
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103 --max-len-diff 0.05
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104 --min-strandedness 0
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105 --min-strand-reads 5
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106 --min-ref-basequal 15
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107 --min-var-basequal 30
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108 --max-basequal-diff 50
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109 --min-ref-mapqual 20
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110 --min-var-mapqual 30
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111 --max-mapqual-diff 10
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112 --max-ref-mmqs 50
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113 --max-var-mmqs 100
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114 --min-mmqs-diff 0
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115 --max-mmqs-diff 50
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116 #elif str($filter_params.settings) == "custom":
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117 --min-var-count2 ${filter_params.min_var_count}
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118 --min-var-count2-lc ${filter_params.min_var_count_lc}
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119 --min-var-count2-depth ${filter_params.min_var_count_depth}
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120 --min-var-freq2 ${filter_params.min_var_freq2}
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121 --min-ref-readpos ${filter_params.min_ref_readpos}
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122 --min-var-readpos ${filter_params.min_var_readpos}
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123 --min-ref-dist3 ${filter_params.min_ref_dist3}
4e97191a1ff7 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit fcf5ac14629c694f0f64773fab0428b1e78fe156"
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124 --min-var-dist3 ${filter_params.min_var_dist3}
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125 --min-ref-len ${filter_params.min_ref_len}
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126 --min-var-len ${filter_params.min_var_len}
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127 --max-len-diff ${filter_params.max_len_diff}
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128 --min-strandedness ${filter_params.min_strandedness}
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129 --min-strand-reads ${filter_params.min_strand_reads}
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130 --min-ref-basequal ${filter_params.min_ref_basequal}
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131 --min-var-basequal ${filter_params.min_var_basequal}
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132 --max-basequal-diff ${filter_params.max_basequal_diff}
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133 --min-ref-mapqual ${filter_params.min_ref_mapqual}
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134 --min-var-mapqual ${filter_params.min_var_mapqual}
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135 --max-mapqual-diff ${filter_params.max_mapqual_diff}
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136 --max-ref-mmqs ${filter_params.max_ref_mmqs}
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137 --max-var-mmqs ${filter_params.max_var_mmqs}
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138 --min-mmqs-diff ${filter_params.min_mmqs_diff}
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139 --max-mmqs-diff ${filter_params.max_mmqs_diff}
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140 #end if
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141 #if $filter_params.experts_only.compat_opts:
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142 #for $opt in str($filter_params.experts_only.compat_opts).split(','):
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143 $opt
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144 #end for
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145 #end if
2
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146 #end if
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147 --verbose
5
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148 '$ref_genome'
0
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149 ]]></command>
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150
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151 <inputs>
2
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152 <conditional name="reference">
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153 <param name="source" type="select"
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154 label="Will you select a reference genome from your history or use a built-in genome?">
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155 <option value="cached">Use a built-in genome</option>
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156 <option value="history">Use a genome from my history</option>
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157 </param>
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158 <when value="cached">
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159 <param name="genome" type="select"
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160 label="reference genome"
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161 help="The fasta reference genome that variants should be called against.">
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162 <options from_data_table="fasta_indexes" />
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163 </param>
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164 </when>
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165 <when value="history">
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166 <param name="genome" type="data" format="fasta"
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167 label="reference genome"
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168 help="The fasta reference genome that variants should be called against."/>
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169 </when>
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170 </conditional>
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171 <param name="normal_bam" type="data" format="bam"
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172 label="aligned reads from normal sample" />
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173 <param name="tumor_bam" type="data" format="bam"
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174 label="aligned reads from tumor sample" />
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175 <param argument="--normal-purity" name="normal_purity" type="float" value="1.0" min="0" max="1.0"
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176 label="Estimated purity (non-tumor content) of normal sample"/>
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177 <param argument="--tumor-purity" name="tumor_purity" type="float" value="1.0" min="0" max="1.0"
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178 label="Estimated purity (tumor content) of tumor sample"/>
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179 <param name="split_output" type="boolean" truevalue="--split-output" falsevalue="" checked="false"
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180 label="Generate separate output datasets for SNP and indel calls?" />
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181 <conditional name="call_params">
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182 <param name="settings" label="Settings for Variant Calling" type="select">
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183 <option value="varscan_defaults" selected="true">Use default values</option>
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184 <option value="custom">Customize settings</option>
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185 </param>
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186 <when value="custom">
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187 <section name="read_selection" title="Read selection" expanded="true"
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188 help="The settings in this section control which mapped reads will be used for variant calling.">
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189 <param argument="samtools mpileup -Q" name="min_basequal" type="integer" value="13" min="1" max="50"
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190 label="Minimum base quality"
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191 help="The minimum base quality (default: 13) at a given position required to use a read for calling variants at that site" />
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192 <param argument="samtools mpileup -q" name="min_mapqual" type="integer" value="0" min="0" max="60"
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193 label="Minimum mapping quality"
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194 help="The minimum mapping quality (default: 0) required for a read to be considered in variant calling" />
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195 <param argument="samtools mpileup -A" name="count_orphans" type="boolean" truevalue="--count-orphans" falsevalue="" checked="false"
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196 label="Use reads from anomalously mapped pairs"
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197 help="Applies to paired-end reads only. If set to true, reads from pairs that are flagged as non-proper pairs (SAM/BAM FLAG field 2) will be used in variant calling. The default is to ignore such reads." />
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198 <param argument="samtools mpileup -x" name="detect_overlaps" type="boolean" truevalue="" falsevalue="--no-detect-overlaps" checked="true"
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199 label="Try to correct for read-pair overlaps"
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200 help="Applies to paired-end reads only. If the reads of a pair overlap on the reference, then with this option (on by default), the bases for which both reads provide evidence will be counted only once in variant calling (of the two sequenced bases in the reads, the base with the better base quality will be used)." />
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201 <param argument="samtools mpileup -d" name="max_pileup_depth" type="integer" value="8000" min="4000"
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202 label="Maximum number of reads per site"
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203 help="Restrict the number of reads used for variant calling at a site to this maximum (default: 8000) for each sample. Helps protect against excessive memory usage (and slow tool runs) at sites of extraordinary high coverage." />
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204 </section>
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205 <expand macro="min_coverage"
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206 help="Minimum site coverage (default: 8) required in the normal and in the tumor sample to call a variant. This threshold gets applied after eliminating reads based on the read selection criteria above." />
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207 <expand macro="min_reads2"
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208 help="Minimum number (default: 2) of variant-supporting reads (after read selection) at a position required to make a call"/>
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209 <expand macro="min_var_freq" value="0.1" />
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210 <expand macro="min_freq_for_hom" />
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211 <expand macro="p_value" value="0.99"
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212 help="The p-value threshold (default: 0.99) used to determine if a variant should be called for either sample" />
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213 <param argument="--somatic-p-value" name="somatic_p_value" type="float" value="0.05" min="0" max="1"
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214 label="P-value threshold for calling somatic variants and LOH events"
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215 help="The p-value threshold (default: 0.05) 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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216 </when>
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217 <when value="varscan_defaults" />
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218 </conditional>
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219 <conditional name="filter_params">
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220 <param name="settings" label="Settings for Posterior Variant Filtering" type="select">
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221 <option value="varscan_defaults" selected="true">Use default values</option>
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222 <option value="dream3_settings">Use settings optimized for DREAM-3</option>
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223 <option value="no_filter">Do not perform posterior filtering</option>
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224 <option value="custom">Customize settings</option>
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225 </param>
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226 <when value="no_filter" />
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227 <when value="varscan_defaults">
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228 <expand macro="filter_compat_options" />
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229 </when>
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230 <when value="dream3_settings">
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231 <expand macro="filter_compat_options" />
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232 </when>
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233 <when value="custom">
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234 <param argument="--min-var-count" name="min_var_count" type="integer" value="4" min="1" max="200"
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235 label="Minimum number of variant-supporting reads"
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236 help="(default: 4)" />
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237 <param argument="--min-var-count-lc" name="min_var_count_lc" type="integer" value="2" min="1" max="200"
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238 label="Low coverage minimum number of variant-supporting reads"
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239 help="This setting (default: 2) will be applied instead of the --min-var-count limit for sites with poor overall (see threshold below) coverage." />
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240 <param argument="--max-somatic-p-depth" name="min_var_count_depth" type="integer" value="10" min="2" max="200"
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241 label="Minimum variant allele count threshold"
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242 help="Combined depth (default: 10) of ref- and variant-supporting reads required at variant site to apply the (stricter) --min-var-count filter instead of --min-var-count-lc" />
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243 <param argument="--min-var-freq" name="min_var_freq2" type="float" value="0.05" min="0" max="1"
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244 label="Minimum variant allele frequency"
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245 help="(default: 0.05)" />
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246 <param argument="--min-ref-readpos" name="min_ref_readpos" type="float" value="0.1" min="0" max="1"
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247 label="Minimum relative variant position in ref-supporting reads"
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248 help="The minimum average relative distance from either end of ref-supporting reads (default: 0.1) required for variant sites" />
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249 <param argument="--min-var-readpos" name="min_var_readpos" type="float" value="0.1" min="0" max="1"
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250 label="Minimum relative variant position in variant-supporting reads"
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251 help="The minimum average relative distance from either end of variant-supporting reads (default: 0.1) required for variant sites" />
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252 <param argument="--min-ref-dist3" name="min_ref_dist3" type="float" value="0.1" min="0" max="1"
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253 label="Minimum distance of variant site from 3'-end of ref-supporting reads"
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254 help="The minimum average relative distance from the effective 3'end of ref-supporting reads (default: 0.1) required for variant sites. The effective 3'end is defined by the end of the alignment of the read to the reference (or, if the Illumina 1.5 compatibility setting is used, by the first base in 3'->5' direction with a base quality > 2)." />
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255 <param argument="--min-var-dist3" name="min_var_dist3" type="float" value="0.1" min="0" max="1"
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256 label="Minimum distance of variant site from 3'-end of variant-supporting reads"
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257 help="The minimum average relative distance from the effective 3'end of variant-supporting reads (default: 0.1) required for variant sites. The effective 3'end is defined as above." />
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258 <param argument="--min-ref-avgrl" name="min_ref_len" type="integer" value="90" min="0" max="200"
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259 label="Minimum length of ref-supporting reads"
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260 help="The minimum average trimmed length (default: 90) required for reads supporting the reference allele" />
2
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261 <param argument="--min-var-avgrl" name="min_var_len" type="integer" value="90" min="0" max="200"
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262 label="Minimum length of variant-supporting reads"
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263 help="The minimum average trimmed length (default: 90) required for reads supporting the variant allele" />
2
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264 <param argument="--max-rl-diff" name="max_len_diff" type="float" value="0.25" min="0" max="1"
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265 label="Maximum relative read length difference"
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266 help="The maximum allowed difference (default: 0.25) in the average relative read length (ref - var) between reads supporting the reference and the variant allele" />
2
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267 <param argument="--min-strandedness" name="min_strandedness" type="float" value="0.01" min="0" max="0.5"
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268 label="Minimum fraction of variant reads from each strand"
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269 help="The minimum fraction (default: 0.01) of variant reads that are required to come from the forward and from the reverse strand" />
2
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270 <param argument="--min-strand-reads" name="min_strand_reads" type="integer" value="5" min="2" max="200"
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271 label="Minimum variant allele depth required to apply the --min-strandedness filter"
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272 help="(default: 5)" />
2
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273 <param argument="--min-ref-basequal" name="min_ref_basequal" type="integer" value="15" min="1" max="50"
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274 label="Minimum average base quality for the ref allele"
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275 help="The minimum average base quality (default: 15) required at the variant site for reads supporting the reference allele" />
2
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276 <param argument="--min-var-basequal" name="min_var_basequal" type="integer" value="15" min="1" max="50"
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277 label="Minimum average base quality for the variant allele"
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278 help="The minimum average base quality (default: 15) required at the variant site for reads supporting the variant allele" />
2
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279 <param argument="max-basequal-diff" name="max_basequal_diff" type="integer" value="50" min="0" max="50"
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280 label="Maximum base quality difference between ref- and variant-supporting reads"
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281 help="The maximum difference (default: 50) in the average base quality (ref - var) allowed between the variant site positions of reads supporting the reference and the variant allele" />
2
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282 <param argument="--min-ref-mapqual" name="min_ref_mapqual" type="integer" value="15" min="1" max="60"
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283 label="Minimum average mapping quality of ref-supporting reads"
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284 help="The minimum average mapping quality (default: 15) required for reads supporting the reference allele" />
2
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285 <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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286 label="Minimum average mapping quality of variant-supporting reads"
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287 help="The minimum average mapping quality (default: 15) required for reads supporting the variant allele" />
2
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288 <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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289 label="Maximum mapping quality difference between ref- and variant-supporting reads"
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290 help="The maximum difference (default: 50) in the average mapping quality (ref - var) allowed between reads supporting the reference and the variant allele" />
2
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291 <param argument="--max-ref-mmqs" name="max_ref_mmqs" type="integer" value="100" min="0"
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292 label="Maximum mismatch base quality sum of ref-supporting reads"
9
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293 help="The maximum mismatch base quality sum (default: 100) allowed for reads supporting the reference allele" />
2
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294 <param argument="--max-var-mmqs" name="max_var_mmqs" type="integer" value="100" min="0"
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295 label="Maximum mismatch base quality sum of var-supporting reads"
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296 help="The maximum mismatch base quality sum (default: 100) allowed for reads supporting the variant allele" />
2
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297 <param argument="--min-mmqs-diff" name="min_mmqs_diff" type="integer" value="0" min="0"
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298 label="Minimum difference between mismatch base quality sums of variant- and ref-supporting reads"
9
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299 help="The minimum difference (default: 0) in the mismatch base quality sums (var - ref) required between reads supporting the variant and the reference allele" />
2
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300 <param argument="--max-mmqs-diff" name="max_mmqs_diff" type="integer" value="50" min="1"
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301 label="Maximum difference between mismatch base quality sums of variant- and ref-supporting reads"
9
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302 help="The maximum difference (default: 50) in the mismatch base quality sums (var - ref) allowed between reads supporting the variant and the reference allele" />
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303 <expand macro="filter_compat_options" />
2
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304 </when>
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305 </conditional>
0
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306 </inputs>
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307 <outputs>
2
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308 <data name="output" format="vcf">
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309 <filter>not split_output</filter>
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310 </data>
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311 <data name="output_snp" from_work_dir="variants_out.snp" format="vcf"
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312 label="Varscan somatic SNP calls on ${on_string}">
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313 <filter>split_output</filter>
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314 </data>
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315 <data name="output_indel" from_work_dir="variants_out.indel" format="vcf"
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316 label="Varscan somatic indel calls on ${on_string}">
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317 <filter>split_output</filter>
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318 </data>
0
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319 </outputs>
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320 <tests>
2
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321 <test expect_num_outputs="1">
9
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322 <!-- run with default settings and genome from history -->
2
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323 <conditional name="reference">
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324 <param name="source" value="history" />
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325 <param name="genome" value="hg19_chrM.fa" />
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326 </conditional>
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327 <param name="normal_bam" value="control_chrM.bam" />
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328 <param name="tumor_bam" value="tumor_chrM.bam" />
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329 <param name="split_output" value="false" />
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330 <conditional name="call_params">
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331 <param name="settings" value="varscan_defaults" />
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332 </conditional>
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333 <conditional name="filter_params">
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334 <param name="settings" value="varscan_defaults" />
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335 </conditional>
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336 <output name="output">
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337 <expand macro="test_mentions_contig" />
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338 <expand macro="test_mentions_filters" />
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339 </output>
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340 </test>
5
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341 <test expect_num_outputs="1">
9
4e97191a1ff7 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit fcf5ac14629c694f0f64773fab0428b1e78fe156"
iuc
parents: 8
diff changeset
342 <!-- run with default settings and cached genome -->
5
d37adcc2ec03 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3a2e62daa15beefe2015ed68cc862b88ade31934
iuc
parents: 2
diff changeset
343 <conditional name="reference">
d37adcc2ec03 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3a2e62daa15beefe2015ed68cc862b88ade31934
iuc
parents: 2
diff changeset
344 <param name="source" value="cached" />
d37adcc2ec03 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3a2e62daa15beefe2015ed68cc862b88ade31934
iuc
parents: 2
diff changeset
345 <param name="genome" value="hg19mito" />
d37adcc2ec03 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3a2e62daa15beefe2015ed68cc862b88ade31934
iuc
parents: 2
diff changeset
346 </conditional>
d37adcc2ec03 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3a2e62daa15beefe2015ed68cc862b88ade31934
iuc
parents: 2
diff changeset
347 <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
iuc
parents: 2
diff changeset
348 <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
iuc
parents: 2
diff changeset
349 <param name="split_output" value="false" />
d37adcc2ec03 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3a2e62daa15beefe2015ed68cc862b88ade31934
iuc
parents: 2
diff changeset
350 <conditional name="call_params">
d37adcc2ec03 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3a2e62daa15beefe2015ed68cc862b88ade31934
iuc
parents: 2
diff changeset
351 <param name="settings" value="varscan_defaults" />
d37adcc2ec03 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3a2e62daa15beefe2015ed68cc862b88ade31934
iuc
parents: 2
diff changeset
352 </conditional>
d37adcc2ec03 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3a2e62daa15beefe2015ed68cc862b88ade31934
iuc
parents: 2
diff changeset
353 <conditional name="filter_params">
d37adcc2ec03 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3a2e62daa15beefe2015ed68cc862b88ade31934
iuc
parents: 2
diff changeset
354 <param name="settings" value="varscan_defaults" />
d37adcc2ec03 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3a2e62daa15beefe2015ed68cc862b88ade31934
iuc
parents: 2
diff changeset
355 </conditional>
d37adcc2ec03 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3a2e62daa15beefe2015ed68cc862b88ade31934
iuc
parents: 2
diff changeset
356 <output name="output">
d37adcc2ec03 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3a2e62daa15beefe2015ed68cc862b88ade31934
iuc
parents: 2
diff changeset
357 <expand macro="test_mentions_contig" />
d37adcc2ec03 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3a2e62daa15beefe2015ed68cc862b88ade31934
iuc
parents: 2
diff changeset
358 <expand macro="test_mentions_filters" />
d37adcc2ec03 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3a2e62daa15beefe2015ed68cc862b88ade31934
iuc
parents: 2
diff changeset
359 </output>
d37adcc2ec03 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3a2e62daa15beefe2015ed68cc862b88ade31934
iuc
parents: 2
diff changeset
360 </test>
2
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents: 1
diff changeset
361 <test expect_num_outputs="2">
9
4e97191a1ff7 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit fcf5ac14629c694f0f64773fab0428b1e78fe156"
iuc
parents: 8
diff changeset
362 <!-- run with default settings and split output -->
2
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents: 1
diff changeset
363 <conditional name="reference">
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents: 1
diff changeset
364 <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
365 <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
366 </conditional>
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents: 1
diff changeset
367 <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
368 <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
369 <param name="split_output" value="true" />
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents: 1
diff changeset
370 <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
371 <param name="settings" value="varscan_defaults" />
1
31a38ce7e8ae planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 33c5694cb2e0a86a76d12a3355a2bd26deba7177
iuc
parents: 0
diff changeset
372 </conditional>
2
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents: 1
diff changeset
373 <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
374 <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
375 </conditional>
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents: 1
diff changeset
376 <output name="output_indel">
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents: 1
diff changeset
377 <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
378 <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
379 </output>
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents: 1
diff changeset
380 <output name="output_snp">
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents: 1
diff changeset
381 <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
382 <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
383 </output>
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents: 1
diff changeset
384 </test>
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents: 1
diff changeset
385 <test expect_num_outputs="1">
9
4e97191a1ff7 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit fcf5ac14629c694f0f64773fab0428b1e78fe156"
iuc
parents: 8
diff changeset
386 <!-- run with custom params for variant calling -->
2
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents: 1
diff changeset
387 <conditional name="reference">
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents: 1
diff changeset
388 <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
389 <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
390 </conditional>
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents: 1
diff changeset
391 <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
392 <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
393 <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
394 <conditional name="call_params">
9
4e97191a1ff7 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit fcf5ac14629c694f0f64773fab0428b1e78fe156"
iuc
parents: 8
diff changeset
395 <section name="read_selection">
4e97191a1ff7 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit fcf5ac14629c694f0f64773fab0428b1e78fe156"
iuc
parents: 8
diff changeset
396 <param name="min_basequal" value="5" />
4e97191a1ff7 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit fcf5ac14629c694f0f64773fab0428b1e78fe156"
iuc
parents: 8
diff changeset
397 </section>
2
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents: 1
diff changeset
398 <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
399 <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
400 <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
401 <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
402 <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
403 <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
404 <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
405 </conditional>
0
72b8ce355fae planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
iuc
parents:
diff changeset
406 <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
407 <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
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="varscan_defaults" />
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents: 1
diff changeset
410 </conditional>
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents: 1
diff changeset
411 <assert_stderr>
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents: 1
diff changeset
412 <has_line_matching
10
a57606054bd7 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 46018cbdd8b4ca124d5c6230862012b9081d56e4"
iuc
parents: 9
diff changeset
413 expression=" *Min coverage:&#09;2x for Normal, 2x for Tumor" />
2
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents: 1
diff changeset
414 <has_line_matching
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents: 1
diff changeset
415 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
416 <has_line_matching
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents: 1
diff changeset
417 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
418 <has_line_matching
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents: 1
diff changeset
419 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
420 <has_line_matching
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents: 1
diff changeset
421 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
422 <has_line_matching
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents: 1
diff changeset
423 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
424 <has_line_matching
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents: 1
diff changeset
425 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
426 <has_line_matching
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents: 1
diff changeset
427 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
428 <has_line_matching
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents: 1
diff changeset
429 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
430 </assert_stderr>
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents: 1
diff changeset
431 <output name="output">
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_mentions_contig" />
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents: 1
diff changeset
433 <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
434 </output>
0
72b8ce355fae planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
iuc
parents:
diff changeset
435 </test>
2
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents: 1
diff changeset
436 <test expect_num_outputs="1">
9
4e97191a1ff7 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit fcf5ac14629c694f0f64773fab0428b1e78fe156"
iuc
parents: 8
diff changeset
437 <!-- run with preconfigured dream3 post-filter settings -->
2
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents: 1
diff changeset
438 <conditional name="reference">
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents: 1
diff changeset
439 <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
440 <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
441 </conditional>
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents: 1
diff changeset
442 <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
443 <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
444 <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
445 <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
446 <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
447 </conditional>
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents: 1
diff changeset
448 <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
449 <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
450 </conditional>
2
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents: 1
diff changeset
451 <output name="output">
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents: 1
diff changeset
452 <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
453 <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
454 </output>
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents: 1
diff changeset
455 </test>
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents: 1
diff changeset
456 <test expect_num_outputs="1">
9
4e97191a1ff7 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit fcf5ac14629c694f0f64773fab0428b1e78fe156"
iuc
parents: 8
diff changeset
457 <!-- run without post-filters -->
2
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents: 1
diff changeset
458 <conditional name="reference">
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents: 1
diff changeset
459 <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
460 <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
461 </conditional>
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents: 1
diff changeset
462 <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
463 <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
464 <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
465 <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
466 <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
467 </conditional>
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents: 1
diff changeset
468 <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
469 <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
470 </conditional>
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents: 1
diff changeset
471 <output name="output">
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents: 1
diff changeset
472 <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
473 <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
474 </output>
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents: 1
diff changeset
475 </test>
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents: 1
diff changeset
476 <test expect_num_outputs="1">
9
4e97191a1ff7 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit fcf5ac14629c694f0f64773fab0428b1e78fe156"
iuc
parents: 8
diff changeset
477 <!-- run with custom post-filters -->
2
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents: 1
diff changeset
478 <conditional name="reference">
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents: 1
diff changeset
479 <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
480 <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
481 </conditional>
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents: 1
diff changeset
482 <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
483 <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
484 <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
485 <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
486 <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
487 </conditional>
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents: 1
diff changeset
488 <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
489 <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
490 <param name="min_ref_basequal" value="28" />
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents: 1
diff changeset
491 <param name="min_var_basequal" value="28" />
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents: 1
diff changeset
492 </conditional>
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents: 1
diff changeset
493 <output name="output">
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents: 1
diff changeset
494 <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
495 <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
496 </output>
1
31a38ce7e8ae planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 33c5694cb2e0a86a76d12a3355a2bd26deba7177
iuc
parents: 0
diff changeset
497 </test>
8
b79bb8b09822 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b
iuc
parents: 6
diff changeset
498 <test expect_num_outputs="1">
b79bb8b09822 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b
iuc
parents: 6
diff changeset
499 <!-- Test with an input bam with extremely high coverage at a
b79bb8b09822 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b
iuc
parents: 6
diff changeset
500 variant site (high enough to trigger an AssertionError from
b79bb8b09822 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b
iuc
parents: 6
diff changeset
501 pysam.libcalignedsegment.get_query_sequences) to see if the
b79bb8b09822 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b
iuc
parents: 6
diff changeset
502 tool can handle this.
b79bb8b09822 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b
iuc
parents: 6
diff changeset
503 Also test that the tool doesn't report SNVs against Ns in
b79bb8b09822 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b
iuc
parents: 6
diff changeset
504 the reference genome (this would lead to more than one variant
b79bb8b09822 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b
iuc
parents: 6
diff changeset
505 getting called). -->
b79bb8b09822 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b
iuc
parents: 6
diff changeset
506 <conditional name="reference">
b79bb8b09822 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b
iuc
parents: 6
diff changeset
507 <param name="source" value="history" />
b79bb8b09822 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b
iuc
parents: 6
diff changeset
508 <param name="genome" value="hg19_chrM.fa" />
b79bb8b09822 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b
iuc
parents: 6
diff changeset
509 </conditional>
b79bb8b09822 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b
iuc
parents: 6
diff changeset
510 <param name="normal_bam" value="high_cov_chrM.bam" />
b79bb8b09822 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b
iuc
parents: 6
diff changeset
511 <param name="tumor_bam" value="high_cov_chrM.bam" />
b79bb8b09822 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b
iuc
parents: 6
diff changeset
512 <param name="split_output" value="false" />
b79bb8b09822 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b
iuc
parents: 6
diff changeset
513 <conditional name="call_params">
b79bb8b09822 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b
iuc
parents: 6
diff changeset
514 <param name="settings" value="varscan_defaults" />
b79bb8b09822 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b
iuc
parents: 6
diff changeset
515 </conditional>
b79bb8b09822 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b
iuc
parents: 6
diff changeset
516 <conditional name="filter_params">
b79bb8b09822 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b
iuc
parents: 6
diff changeset
517 <param name="settings" value="varscan_defaults" />
b79bb8b09822 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b
iuc
parents: 6
diff changeset
518 </conditional>
b79bb8b09822 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b
iuc
parents: 6
diff changeset
519 <output name="output">
b79bb8b09822 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b
iuc
parents: 6
diff changeset
520 <expand macro="test_mentions_contig" />
b79bb8b09822 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b
iuc
parents: 6
diff changeset
521 <expand macro="test_mentions_filters" />
b79bb8b09822 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b
iuc
parents: 6
diff changeset
522 <metadata name="data_lines" value="1" />
b79bb8b09822 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b
iuc
parents: 6
diff changeset
523 </output>
b79bb8b09822 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b
iuc
parents: 6
diff changeset
524 </test>
0
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525 </tests>
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526
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527 <help>
2
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528 @HELP_HEADER@
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diff changeset
529
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diff changeset
530 **The Varscan Somatic tool for Galaxy**
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parents: 1
diff changeset
531
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diff changeset
532 This tool wraps the functionality of the ``varscan somatic`` and the
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
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diff changeset
533 ``varscan fpfilter`` command line tools.
0
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diff changeset
534
2
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parents: 1
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535 The tool is designed to detect genetic variants in a **pair of samples**
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parents: 1
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536 representing normal and tumor tissue from the same individual. It classifies
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parents: 1
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537 the variants, according to their most likely origin, as **somatic** (variant is
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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538 found in the tumor, but not in the normal sample, *i.e.*, is the consequence of
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539 a somatic mutation event), **germline** (variant is found in both samples =>
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540 germline mutation event) and **LOH** (variant is found in both samples, but
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541 only the tumor sample appears to be homozygous for it => loss of heterozygosity
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542 event).
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543 This classification is encoded in the variant ``INFO`` fields of the VCF output
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544 produced by the tool in the form of a status code ``SS`` (somatic status),
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parents: 1
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545 where:
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546
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547 - ``SS=1`` signifies a likely germline variant,
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548 - ``SS=2`` a somatic variant
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549 - ``SS=3`` a LOH variant
0
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550
2
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551 In addition, ``SS=0`` indicates a possible variant, but with insufficient
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
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552 evidence for an, at least, heterozygous state in either individual sample, and
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553 ``SS=5`` is used for variants of unexplained origin (*e.g.*, variants found in
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
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554 the normal, but not in the tumor tissue sample).
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parents: 1
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555
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556 In a second step, following variant calling, the tool can try to detect likely
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
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557 false-positive calls by re-inspecting the data at the variant sites more
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558 carefully and looking for signs that may indicate problems with the
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559 sequencing data or its mapping. If a called variant is deemed a possible
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560 false-positive at this step, this gets indicated in the ``FILTER`` field of the
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561 variant record in the VCF output. For high confidence variants passing all
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
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562 posterior (applied after variant calling) filters the value of the field will
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563 be ``PASS``, for variants failing any of the posterior filters the value will
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564 be a ``;``-separated list of the problematic filters.
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565
0
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diff changeset
566
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567 **Input**
72b8ce355fae planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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568
2
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569 The tool takes as input a reference genome (in fasta format) and a pair of
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diff changeset
570 aligned reads datasets (bam format).
0
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571
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572 **Output**
72b8ce355fae planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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573
2
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574 A VCF dataset of called variants. When asked to *Generate separate output
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
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575 datasets for SNP and indel calls*, the tool will behave like the
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576 ``varscan somatic`` command line tool and produce two VCF datasets - one with
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
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577 just the single nucleotide variants, while the other one will store
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
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diff changeset
578 insertion/deletion variants.
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diff changeset
579
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580 **Options**
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diff changeset
581
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582 *Estimated purity of normal sample / of tumor sample*
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583
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584 Since, in practice, it is often impossible to isolate tissue samples without
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
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585 contamination from surrounding tissue or from invading cells, these two fields
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
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586 let you indicate your estimate of the purity of the two samples (as fractions
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587 between 0 and 1, where 1 would indicate a contamination-free sample and 0.5 a
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588 sample to which the desired tissue contributes only 50%, while the other 50%
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589 consist of cells from the other tissue type).
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590
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591 *Settings for Variant Calling*
0
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592
2
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593 Settings in this section will affect the steps of variant calling and
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594 classification. You can accept VarScan's default values for the corresponding
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595 parameters or customize them according to your needs.
0
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596
2
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597 *Settings for Posterior Variant Filtering*
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598
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599 Use the parameters in this section to configure the false-positive filtering
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600 step that follows variant calling and classification. These settings will not
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601 influence the number of variants detected nor their classification, but may
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602 change the ``FILTER`` field of variant records to indicate which variants
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603 failed to pass certain filters. You can use this information with downstream
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604 tools to exclude certain variants from further analysis steps or include only
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605 high confidence variants that passed all filters (those with ``PASS`` as their
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606 ``INFO`` field value. You can accept the orignal filter defaults of the
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607 ``varscan fpfilter`` command line tool, use the settings established for the
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608 tool in the `DREAM3 challenge`_, or choose to customize the settings.
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609 Alternatively, you can also choose to skip posterior filtering entirely, in
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610 which case all variants will have their ``INFO`` field set to ``PASS``.
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611
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612 .. _DREAM3 challenge: https://www.synapse.org/#!Synapse:syn312572/wiki/58893
0
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613 </help>
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614 <expand macro="citations" />
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615 </tool>