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1 <tool id="varscan_somatic" name="VarScan Somatic" version="2.3.5">
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2 <description>
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3 somatic mutation caller for cancer genomics
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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 varscan_somatic.pl
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10 "COMMAND::java -jar \$JAVA_JAR_PATH/VarScan.v2.3.5.jar somatic"
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11 "NORMAL::$normal"
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12 "TUMOR::$tumor"
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13 "OUTPUT::$output"
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14
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15 "OPTION::--min-coverage $min_coverage"
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16 "OPTION::--min-coverage-normal $min_coverage_normal"
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17 "OPTION::--min-coverage-tumor $min_coverage_tumor"
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18
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19 "OPTION::--min-var-freq $min_var_freq"
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20 "OPTION::--min-freq-for-hom $min_freq_for_hom"
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21
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22 "OPTION::--normal-purity $normal_purity"
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23 "OPTION::--tumor-purity $tumor_purity"
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24
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25 "OPTION::--p-value $p_value"
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26 "OPTION::--somatic-p-value $somatic_p_value"
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27
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28 "OPTION::--strand-filter $strand_filter"
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29 "OPTION::--validation $validation"
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30 "OPTION::--output-vcf 1"
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31
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32
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33
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34 </command>
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35
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36 <inputs>
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37
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38 <param name="normal" type="data" format="pileup" label="normal mpileup file" help="The SAMtools mpileup file for normal sample" />
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39 <param name="tumor" type="data" format="pileup" label="tumor mpileup file" help="The SAMtools mpileup file for tumor sample" />
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40
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41 <param name="min_coverage" type="integer" label="min-coverage" help="" optional="true" value="8"/>
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42 <param name="min_coverage_normal" type="integer" label="min-coverage-normal" help="" optional="true" value="8"/>
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43 <param name="min_coverage_tumor" type="integer" label="min-coverage-tumor" help="" optional="true" value="6"/>
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44
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45 <param name="min_var_freq" type="float" label="min-var-freq" help="" optional="true" value="0.10"/>
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46 <param name="min_freq_for_hom" type="float" label="min-freq-for-hom" help="" optional="true" value="0.75"/>
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47
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48 <param name="normal_purity" type="float" label="normal-purity" help="" optional="true" value="1.00"/>
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49 <param name="tumor_purity" type="float" label="tumor-purity" help="" optional="true" value="1.00"/>
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50
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51
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52 <param name="p_value" type="text" label="p-value" help="" optional="true" value="0.99"/>
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53 <param name="somatic_p_value" type="text" label="somatic-p-value" help="" optional="true" value="0.05"/>
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54
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55 <param name="strand_filter" type="integer" label="strand-filter" help="" optional="true" value="1"/>
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56 <param name="validation" type="integer" label="validation" help="" optional="true" value="0"/>
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57
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58 </inputs>
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59 <outputs>
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60 <data type="data" format="vcf" name="output" label="${tool.name} result on ${on_string}"/>
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61 </outputs>
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62
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63 <help>
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64
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65 .. class:: infomark
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66
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67 **What it does**
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68
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69 ::
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70
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71 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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72
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73 Germline variants (SNPs an dindels) in individual samples or pools of samples.
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74 Multi-sample variants (shared or private) in multi-sample datasets (with mpileup).
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75 Somatic mutations, LOH events, and germline variants in tumor-normal pairs.
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76 Somatic copy number alterations (CNAs) in tumor-normal exome data.
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77
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78
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79 **Input**
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80
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81 ::
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82
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83 mpileup normal file - The SAMtools mpileup file for normal
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84 mpileup tumor file - The SAMtools mpileup file for tumor
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85
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86
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87 **Parameters**
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88
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89 ::
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90
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91 min-coverage
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92 Minimum read depth at a position to make a call [8]
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93
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94 min-coverage-normal
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95 Minimum coverage in normal to call somatic [8]
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96
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97 min-coverage-tumor
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98 Minimum coverage in tumor to call somatic [6]
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99
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100 min-var-freq
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101 Minimum variant frequency to call a heterozygote [0.10]
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102
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103 min-freq-for-hom
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104 Minimum frequency to call homozygote [0.75]
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105
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106 normal-purity
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107 Estimated purity (non-tumor content) of normal sample [1.00]
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108
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109 tumor-purity
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110 Estimated purity (tumor content) of tumor sample [1.00]
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111
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112 p-value
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113 Default p-value threshold for calling variants [0.99]
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114
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115 somatic-p-value
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116 P-value threshold to call a somatic site [0.05]
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117
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118 strand-filter
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119 If set to 1, removes variants with >90% strand bias
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120
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121 validation
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122 If set to 1, outputs all compared positions even if non-variant
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123
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124 output-vcf
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125 If set to 1, outputs in VCF format [Default]
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126
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127
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128
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129 </help>
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130 </tool>
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131
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