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1 <tool id="muTect" name="muTect" version="1.0.0">
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2 <description>identify somatic point mutations</description>
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3 <requirements>
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2
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4 <requirement type="set_environment" version="1.0">MUTECTPATH</requirement>
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1
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5 </requirements>
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6 <command interpreter="java">
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7 -Xmx2g -jar \$MUTECTPATH/muTect-1.1.1.jar
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8 --analysis_type MuTect
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9 --reference_sequence $reference
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10 #if ($cosmic.has_cosmic):
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11 --cosmic $cosmic.cosmicfile
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12 #end if
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13 --dbsnp $dbsnp
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14 #if str($intervals) != ""
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15 --intervals $intervals
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16 #end if
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17 #if str($intervals) == "" and str($intervalfile) != ""
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18 --intervals $intervalfile
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19 #end if
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20 --input_file:normal $normal
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21 --input_file:tumor $tumor
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22 --out call_stats.txt
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23 --coverage_file coverage.wig.txt
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24 </command>
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25
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26 <inputs>
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27 <param name="reference" type="data" format="bed, fasta" label="Select a reference genome">
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28 </param>
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29 <param name="dbsnp" type="data" format="vcf" label="dbsnp.vcf file" />
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30 <param name="intervals" type="text" label="Intervals to process" help="In format 'chr1:1500-2500; chr2:2500-3500', separated by semicolons" optional="true"/>
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31 <param name="intervalfile" type="data" format="txt" label="Intervals to process (.txt file)" help="'chr1:1500-2500', one entry per line" optional="true"/>
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32 <param name="normal" type="bam" label="Normal BAM file"/>
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33 <param name="tumor" type="bam" label="Tumor BAM file"/>
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34 <conditional name="cosmic">
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35 <param name="has_cosmic" type="boolean" label="Cosmic vcf file available for specimen" value="false" />
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36 <when value="true">
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37 <param name="cosmicfile" type="data" format="vcf" label="Cosmic vcf file"/>
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38 </when>
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39 </conditional>
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40
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41
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42 </inputs>
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43
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44 <outputs>
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45 <data format="txt" name="callstats" label="Detailed caller output" from_work_dir="call_stats.txt"/>
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46 <data format="txt" name="coverage" label="Filename for coverage output" from_work_dir="coverage.wig.txt"/>
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47 </data>
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48 </outputs>
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49
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50 <help>
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51
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52 .. class:: infomark
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53
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54 **License**
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55
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56 TmuTect Revision: 44830
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57 GATK Revision: 2.1-202-g2fe6a31
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58 Copyright (c) 2012 The Broad Institute
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59 Please view our documentation at http://www.broadinstitute.org/gsa/wiki
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60 For support, please view our support site at http://getsatisfaction.com/gsa
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61
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62 **What it does**
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63
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64 MuTect is a method developed at the Broad Institute for the reliable
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65 and accurate identification of somatic point mutations in next generation
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66 sequencing data of cancer genomes.
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67
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68
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69
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70 **Input**
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71
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72 Reference Genome:
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73
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74 Fasta file of ref gnome
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75
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76 Normal Sample:
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77
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78 bam normal sample
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79
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80 Tumor Sample:
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81
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82 bam tumor sample
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83
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84
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85 Intervals:
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86
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87 A list of genomic intervals over which to operate.
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88
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89
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90
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91 **Output**
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92
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93 Caller Output:
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94
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95 Detailed caller output
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96
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97 Coverage Output:
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98
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99 write out coverage in WIGGLE format to this file
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100
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101
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102 </help>
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103 </tool>
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104
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105
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106
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107
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