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1 <tool id="varscan_processSomatic" name="ProcessSomatic" version="2.3.5">
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2 <description>
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3 Extract HC calls from Somatic Caller
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4 </description>
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5 <requirements>
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6 <requirement type="package" version="2.3.5">VarScan</requirement>
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7 </requirements>
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8 <command interpreter="perl">
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9
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10 varscan_processSomatic.pl
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11 "COMMAND::java -jar \$JAVA_JAR_PATH/VarScan.v2.3.5.jar processSomatic"
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12 "INPUT::$input"
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13 "LOG::$log"
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14
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15 "OPTION::--min-tumor-freq $min_tumor_freq"
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16 "OPTION::--max-normal-freq $max_normal_freq"
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17 "OPTION::--p-value $p_value"
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18 "OUTPUT::--loh $loh"
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19 "OUTPUT::--loh_hc $loh_hc"
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20 "OUTPUT::--germ $germ"
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21 "OUTPUT::--germ_hc $germ_hc"
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22 "OUTPUT::--som $som"
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23 "OUTPUT::--som_hc $som_hc"
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24 "OUTPUT::--som_hc_vcf $som_hc_vcf"
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25 "OUTPUT::--germ_hc_vcf $germ_hc_vcf"
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26 "OUTPUT::--loh_hc_vcf $loh_hc_vcf"
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27
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28 </command>
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29
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30 <inputs>
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31
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32 <param name="input" type="data" format="txt" label="Input File" help="VarScan Somatics output file in native format" />
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33
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34 <param name="min_tumor_freq" type="float" label="min-tumor-freq" help="Minimum variant allele frequency in tumor" optional="true" value="0.10"/>
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35 <param name="max_normal_freq" type="float" label="max-normal-freq" help="Maximum variant allele frequency in normal" optional="true" value="0.05"/>
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36 <param name="p_value" type="text" label="p-value" help="P-value for high-confidence calling" optional="true" value="0.07"/>
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37 <param name="outtype" type="select" label="Output Type:" default="1">
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38 <option value="0">Native VarScan Tables</option>
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39 <option value="1">VCF format (only High Confidence)</option>
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40 <option value="2">Both</option>
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41 </param>
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42
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43 </inputs>
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44 <outputs>
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45 <data type="data" format="txt" name="log" label="${tool.name} result on ${on_string} (log) " />
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46 <data type="data" format="txt" name="loh" label="${tool.name} result on ${on_string} (loh) " >
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47 <filter>outtype != "1"</filter>
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48 </data>
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49 <data type="data" format="txt" name="loh_hc" label="${tool.name} result on ${on_string} (loh_hc)">
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50 <filter>outtype != "1"</filter>
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51 </data>
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52
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53 <data type="data" format="txt" name="germ" label="${tool.name} result on ${on_string} (germline)" >
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54 <filter>outtype != "1"</filter>
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55 </data>
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56
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57 <data type="data" format="txt" name="germ_hc" label="${tool.name} result on ${on_string} (germline_hc)">
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58 <filter>outtype != "1"</filter>
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59 </data>
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60
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61 <data type="data" format="txt" name="som" label="${tool.name} result on ${on_string} (somatic)" >
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62 <filter>outtype != "1"</filter>
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63 </data>
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64
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65 <data type="data" format="txt" name="som_hc" label="${tool.name} result on ${on_string} (somatic_hc)" >
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66 <filter>outtype != "1"</filter>
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67 </data>
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68
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69 <data type="data" format="vcf" name="som_hc_vcf" label="${tool.name} result on ${on_string} (Somatic_HC.vcf)" >
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70 <filter>outtype != "0"</filter>
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71 </data>
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72
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73 <data type="data" format="vcf" name="loh_hc_vcf" label="${tool.name} result on ${on_string} (LOH_HC.vcf)" >
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74 <filter>outtype != "0"</filter>
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75 </data>
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76
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77 <data type="data" format="vcf" name="germ_hc_vcf" label="${tool.name} result on ${on_string} (Germline_HC.vcf)" >
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78 <filter>outtype != "0"</filter>
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79 </data>
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80
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81
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82
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83
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84 </outputs>
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85
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86 <help>
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87
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88 .. class:: infomark
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89
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90 **What it does**
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91
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92 ::
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93
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94 VarScan is a platform-independent mutation caller for targeted, exome, and whole-genome resequencing data generated on Illumina, SOLiD, Life/PGM, Roche/454, and similar instruments. The newest version, VarScan 2, is written in Java, so it runs on most operating systems. It can be used to detect different types of variation:
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95
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96 Germline variants (SNPs an dindels) in individual samples or pools of samples.
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97 Multi-sample variants (shared or private) in multi-sample datasets (with mpileup).
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98 Somatic mutations, LOH events, and germline variants in tumor-normal pairs.
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99 Somatic copy number alterations (CNAs) in tumor-normal exome data.
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100
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101
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102 **Input**
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103
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104 ::
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105
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106 mpileup normal file - The SAMtools mpileup file for normal
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107 mpileup tumor file - The SAMtools mpileup file for tumor
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108
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109
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110 **Parameters**
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111
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112 ::
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113
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114 min-coverage
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115 Minimum read depth at a position to make a call [8]
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116
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117 min-coverage-normal
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118 Minimum coverage in normal to call somatic [8]
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119
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120 min-coverage-tumor
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121 Minimum coverage in tumor to call somatic [6]
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122
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123 min-var-freq
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124 Minimum variant frequency to call a heterozygote [0.10]
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125
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126 min-freq-for-hom
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127 Minimum frequency to call homozygote [0.75]
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128
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129 normal-purity
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130 Estimated purity (non-tumor content) of normal sample [1.00]
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131
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132 tumor-purity
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133 Estimated purity (tumor content) of tumor sample [1.00]
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134
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135 p-value
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136 Default p-value threshold for calling variants [0.99]
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137
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138 somatic-p-value
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139 P-value threshold to call a somatic site [0.05]
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140
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141 strand-filter
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142 If set to 1, removes variants with >90% strand bias
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143
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144 validation
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145 If set to 1, outputs all compared positions even if non-variant
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146
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147 output-vcf
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148 If set to 1, outputs in VCF format [Default]
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149
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150
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151
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152 </help>
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153 </tool>
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154
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