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1 <tool id="varscan_somatic" name="VarScan Somatic (Native Output)" 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
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10 varscan_somatic.pl
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11 "COMMAND::java -jar \$JAVA_JAR_PATH/VarScan.v2.3.5.jar somatic"
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12 "NORMAL::$normal"
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13 "TUMOR::$tumor"
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14 "TUMORBAM::$tumorbam"
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15 "SNP::$snp"
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16 "INDEL::$indel"
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17 "LOG::$log"
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18
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19 "OPTION::--min-coverage $min_coverage"
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20 "OPTION::--min-coverage-normal $min_coverage_normal"
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21 "OPTION::--min-coverage-tumor $min_coverage_tumor"
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22
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23 "OPTION::--min-var-freq $min_var_freq"
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24 "OPTION::--min-freq-for-hom $min_freq_for_hom"
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25
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26 "OPTION::--normal-purity $normal_purity"
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27 "OPTION::--tumor-purity $tumor_purity"
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28
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29 "OPTION::--p-value $p_value"
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30 "OPTION::--somatic-p-value $somatic_p_value"
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31
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32 "OPTION::--strand-filter $strand_filter"
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33 "OPTION::--validation $validation"
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34
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35
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36
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37 </command>
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38
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39 <inputs>
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40
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41 <param name="normal" type="data" format="pileup" label="normal mpileup file" help="The SAMtools mpileup file for normal sample" />
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42 <param name="tumor" type="data" format="pileup" label="tumor mpileup file" help="The SAMtools mpileup file for tumor sample" />
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43 <param name="tumorbam" type="data" format="bam" label="tumor BAM file" help="The BAM file of the tumor sample used in mpileup step" />
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44
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45 <param name="min_coverage" type="integer" label="min-coverage" help="" optional="true" value="8"/>
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46 <param name="min_coverage_normal" type="integer" label="min-coverage-normal" help="" optional="true" value="8"/>
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47 <param name="min_coverage_tumor" type="integer" label="min-coverage-tumor" help="" optional="true" value="6"/>
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48
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49 <param name="min_var_freq" type="float" label="min-var-freq" help="" optional="true" value="0.10"/>
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50 <param name="min_freq_for_hom" type="float" label="min-freq-for-hom" help="" optional="true" value="0.75"/>
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51
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52 <param name="normal_purity" type="float" label="normal-purity" help="" optional="true" value="1.00"/>
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53 <param name="tumor_purity" type="float" label="tumor-purity" help="" optional="true" value="1.00"/>
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54
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55
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56 <param name="p_value" type="text" label="p-value" help="" optional="true" value="0.99"/>
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57 <param name="somatic_p_value" type="text" label="somatic-p-value" help="" optional="true" value="0.05"/>
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58
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59 <param name="strand_filter" type="integer" label="strand-filter" help="" optional="true" value="1"/>
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60 <param name="validation" type="integer" label="validation" help="" optional="true" value="0"/>
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61
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62 </inputs>
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63 <outputs>
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64 <data type="data" format="txt" name="log" label="${tool.name} result on ${on_string} (log) "/>
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65 <data type="data" format="txt" name="snp" label="${tool.name} result on ${on_string} (SNP)" />
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66 <data type="data" format="txt" name="indel" label="${tool.name} result on ${on_string} (INDEL)" />
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67
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68
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69 </outputs>
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70
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71 <help>
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72
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73 .. class:: infomark
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74
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75 **What it does**
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76
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77 ::
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78
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79 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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80
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81 Germline variants (SNPs an dindels) in individual samples or pools of samples.
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82 Multi-sample variants (shared or private) in multi-sample datasets (with mpileup).
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83 Somatic mutations, LOH events, and germline variants in tumor-normal pairs.
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84 Somatic copy number alterations (CNAs) in tumor-normal exome data.
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85
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86
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87 **Input**
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88
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89 ::
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90
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91 mpileup normal file - The SAMtools mpileup file for normal
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92 mpileup tumor file - The SAMtools mpileup file for tumor
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93
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94
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95 **Parameters**
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96
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97 ::
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98
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99 min-coverage
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100 Minimum read depth at a position to make a call [8]
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101
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102 min-coverage-normal
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103 Minimum coverage in normal to call somatic [8]
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104
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105 min-coverage-tumor
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106 Minimum coverage in tumor to call somatic [6]
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107
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108 min-var-freq
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109 Minimum variant frequency to call a heterozygote [0.10]
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110
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111 min-freq-for-hom
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112 Minimum frequency to call homozygote [0.75]
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113
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114 normal-purity
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115 Estimated purity (non-tumor content) of normal sample [1.00]
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116
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117 tumor-purity
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118 Estimated purity (tumor content) of tumor sample [1.00]
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119
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120 p-value
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121 Default p-value threshold for calling variants [0.99]
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122
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123 somatic-p-value
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124 P-value threshold to call a somatic site [0.05]
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125
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126 strand-filter
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127 If set to 1, removes variants with >90% strand bias
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128
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129 validation
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130 If set to 1, outputs all compared positions even if non-variant
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131
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132 output-vcf
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133 If set to 1, outputs in VCF format [Default]
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134
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135
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136
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137 </help>
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138 </tool>
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139
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