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1 <tool id="varscan_somatic" name="VarScan Somatic (VCF 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::$tumorbam"
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15 "OUTPUT::$output"
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16 "LOG::$log"
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17
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18 "OPTION::--min-coverage $min_coverage"
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19 "OPTION::--min-coverage-normal $min_coverage_normal"
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20 "OPTION::--min-coverage-tumor $min_coverage_tumor"
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21
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22 "OPTION::--min-var-freq $min_var_freq"
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23 "OPTION::--min-freq-for-hom $min_freq_for_hom"
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24
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25 "OPTION::--normal-purity $normal_purity"
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26 "OPTION::--tumor-purity $tumor_purity"
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27
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28 "OPTION::--p-value $p_value"
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29 "OPTION::--somatic-p-value $somatic_p_value"
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30
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31 "OPTION::--strand-filter $strand_filter"
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32 "OPTION::--validation $validation"
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33 "OPTION::--output-vcf 1"
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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="vcf" name="output" label="${tool.name} result on ${on_string}"/>
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65 <data type="data" format="txt" name="log" label="${tool.name} result on ${on_string} (log) "/>
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66 <!--<data type="data" format="txt" name="snp" label="${tool.name} result on ${on_string} (SNP file)" />
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67 <data type="data" format="txt" name="indel" label="${tool.name} result on ${on_string} (INDEL file)" />-->
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68
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69
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70 </outputs>
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71
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72 <help>
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73
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74 .. class:: infomark
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75
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76 **What it does**
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77
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78 ::
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79
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80 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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81
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82 Germline variants (SNPs an dindels) in individual samples or pools of samples.
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83 Multi-sample variants (shared or private) in multi-sample datasets (with mpileup).
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84 Somatic mutations, LOH events, and germline variants in tumor-normal pairs.
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85 Somatic copy number alterations (CNAs) in tumor-normal exome data.
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86
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87
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88 **Input**
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89
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90 ::
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91
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92 mpileup normal file - The SAMtools mpileup file for normal
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93 mpileup tumor file - The SAMtools mpileup file for tumor
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94
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95
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96 **Parameters**
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97
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98 ::
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99
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100 min-coverage
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101 Minimum read depth at a position to make a call [8]
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102
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103 min-coverage-normal
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104 Minimum coverage in normal to call somatic [8]
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105
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106 min-coverage-tumor
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107 Minimum coverage in tumor to call somatic [6]
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108
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109 min-var-freq
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110 Minimum variant frequency to call a heterozygote [0.10]
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111
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112 min-freq-for-hom
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113 Minimum frequency to call homozygote [0.75]
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114
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115 normal-purity
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116 Estimated purity (non-tumor content) of normal sample [1.00]
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117
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118 tumor-purity
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119 Estimated purity (tumor content) of tumor sample [1.00]
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120
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121 p-value
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122 Default p-value threshold for calling variants [0.99]
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123
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124 somatic-p-value
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125 P-value threshold to call a somatic site [0.05]
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126
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127 strand-filter
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128 If set to 1, removes variants with >90% strand bias
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129
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130 validation
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131 If set to 1, outputs all compared positions even if non-variant
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132
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133 output-vcf
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134 If set to 1, outputs in VCF format [Default]
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135
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136
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137
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138 </help>
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139 </tool>
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140
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