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1 <tool id="varscan_mpileup" name="VarScan mpileup" version="2.3.5">
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2 <description>
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3 mutation caller for targeted, exome, and whole-genome resequencing
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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_mpileup.pl
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11 "COMMAND::java -jar \$JAVA_JAR_PATH/VarScan.v2.3.5.jar $exe_command"
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12 "INPUT::$in_file"
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13 "OUTPUT::$output"
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14 "LOG::$log"
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15 "OPTION::--min-coverage $min_coverage"
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16 "OPTION::--min-reads2 $min_reads2"
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17 "OPTION::--min-avg-qual $min_avg_qual"
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18 "OPTION::--min-var-freq $min_var_freq"
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19 "OPTION::--min-freq-for-hom $min_freq_for_hom"
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20 "OPTION::--p-value $p_value"
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21 "OPTION::--strand-filter $strand_filter"
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22 "OPTION::--output-vcf 1"
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23
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24 #if ($vcf_sample_list):
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25 "OPTION::--vcf-sample-list $vcf_sample_list"
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26 #end if
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27 "OPTION::--variants $variants"
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28
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29
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30
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31 </command>
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32
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33 <inputs>
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34
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35 <param name="exe_command" type="select" label="Command" help="" optional="false">
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36 <option value="mpileup2snp" >mpileup2snp</option>
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37 <option value="mpileup2indel">mpileup2indel</option>
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38 <option value="mpileup2cns">mpileup2cns</option>
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39 </param>
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40 <param name="in_file" type="data" format="pileup" label="mpileup file" help="The SAMtools mpileup file" />
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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_reads2" type="integer" label="min-reads2" help="" optional="true" value="2"/>
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43 <param name="min_avg_qual" type="integer" label="min-avg-qual" help="" optional="true" value="15"/>
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44 <param name="min_var_freq" type="float" label="min-var-freq" help="" optional="true" value="0.01"/>
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45 <param name="min_freq_for_hom" type="float" label="min-freq-for-hom" help="" optional="true" value="0.75"/>
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46 <param name="p_value" type="text" label="p-value" help="" optional="true" value="0.99"/>
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47 <param name="strand_filter" type="integer" label="strand-filter" help="" optional="true" value="1"/>
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48 <param name="vcf_sample_list" type="data" label="vcf-sample-list" format="txt" help="" optional="true" />
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49 <param name="variants" type="integer" label="variants" help="Set to 1 to report only variants" optional="true" value="1"/>
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50
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51
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52 </inputs>
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53 <outputs>
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54 <data type="data" format="vcf" name="output" label="${tool.name} result on ${on_string}"/>
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55 <data type="data" format="txt" name="log" label="${tool.name} result on ${on_string} (log) "/>
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56 </outputs>
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57
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58 <help>
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59
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60 .. class:: infomark
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61
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62 **What it does**
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63
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64 ::
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65
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66 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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67
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68 Germline variants (SNPs an dindels) in individual samples or pools of samples.
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69 Multi-sample variants (shared or private) in multi-sample datasets (with mpileup).
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70 Somatic mutations, LOH events, and germline variants in tumor-normal pairs.
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71 Somatic copy number alterations (CNAs) in tumor-normal exome data.
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72
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73
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74 **Input**
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75
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76 ::
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77
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78 mpileup file - The SAMtools mpileup file
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79
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80
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81 **Parameters**
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82
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83 ::
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84
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85 commands
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86 mpileup2snp Identify SNPs from an mpileup file
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87 mpileup2indel Identify indels an mpileup file
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88 mpileup2cns Call consensus and variants from an mpileup file
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89
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90 min-coverage
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91 Minimum read depth at a position to make a call [8]
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92
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93 min-reads2
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94 Minimum supporting reads at a position to call variants [2]
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95
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96 min-avg-qual
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97 Minimum base quality at a position to count a read [15]
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98
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99 min-var-freq
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100 Minimum variant allele frequency threshold [0.01]
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101
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102 min-freq-for-hom
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103 Minimum frequency to call homozygote [0.75]
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104
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105 p-value
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106 Default p-value threshold for calling variants [99e-02]
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107
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108 strand-filter
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109 Ignore variants with >90% support on one strand [1]
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110
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111 output-vcf
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112 If set to 1, outputs in VCF format
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113
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114 vcf-sample-list
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115 For VCF output, a list of sample names in order, one per line
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116
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117 variants
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118 Report only variant (SNP/indel) positions [0]
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119
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120
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121
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122 </help>
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123 </tool>
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124
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