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1 <tool id="MutSpecfilter" name="MutSpec Filter" version="0.1" hidden="false">
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2 <description>Filter out variants present in public databases</description>
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3
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4 <requirements>
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5 <requirement type="set_environment">SCRIPT_PATH</requirement>
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6 <requirement type="package" version="5.18.1">perl</requirement>
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7 </requirements>
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8
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9 <command interpreter="perl">
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10 mutspecFilter.pl
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11 --dir \$SCRIPT_PATH
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12 $segDup
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13 $esp
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14 $thG
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1
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15 #if $FilterdbSNP.dbSNP == True:
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0
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16 --dbSNP ${FilterdbSNP.column}
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17 #else
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18 --dbSNP 0
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19 #end if
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20 --refGenome ${refGenome}
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21 --outfile $output
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22 $input
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23 </command>
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24
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25 <inputs>
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26 <param name="input" type="data" format="txt" label="Input file"/>
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27
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28 <param name="refGenome" type="select" label="Reference genome" help="All your data should have been annotated with the selected genome">
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29 <options from_data_table="annovar_index" />
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30 </param>
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31
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32 <conditional name="FilterdbSNP">
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33 <param name="dbSNP" type="boolean" checked="true" truevalue="true" label="Filter against dbSNP database" help="Remove variants with a RS number" />
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34 <when value="true">
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35 <param name="column" type="data_column" data_ref="input" label="Select the dbSNP column for filtering" use_header_names="true" help="Select a column name snp or snpNonFlagged" />
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36 </when>
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37 </conditional>
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38
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39
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40 <param name="segDup" type="boolean" checked="true" truevalue="--segDup" falsevalue="" label="Filter against SegDup database" help="Remove variants present at >= 0.9 frequency in the genomic duplicate segments database" />
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41 <param name="esp" type="boolean" checked="true" truevalue="--esp" falsevalue="" label="Filter against the ESP database" help="Remove variants present at frequency > 0.001 in the Exome Sequencing Project database (only valid for human genomes)" />
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42 <param name="thG" type="boolean" checked="true" truevalue="--thG" falsevalue="" label="Filter against the 1000g database project" help="Remove variants present at frequency > 0.001 in the 1000 genome database (only valid for human genomes)" />
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43 </inputs>
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44
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45 <outputs>
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46 <data type="data" name="output" format="tabular" label="${input.name.split(' ')[0]} filtered" />
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47 </outputs>
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48
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49 <help>
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50
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51 **What it does**
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52
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53 Filter a file annotated with MutSpec-Annot tool. Variants present in public databases (dbSNP, SegDup, ESP, 1000 genome obtained from Annovar) will be removed from the input file (with frequency limits described above).
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54
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55 .. class:: warningmark
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56
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57 The databases ESP and 1000 genome can be used only for human genomes
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58
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59 --------------------------------------------------------------------------------------------------------------------------------------------------
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60
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61 **Input**
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62
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63 .. class:: warningmark
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64
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65 Tab delimited text files generated by MutSpec-Annot tool.
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66
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67 --------------------------------------------------------------------------------------------------------------------------------------------------
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68
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69 **Output**
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70
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71 Tab delimited text file filtered for variants considered as neutral polymorphisms.
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72
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73 --------------------------------------------------------------------------------------------------------------------------------------------------
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74
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75 **Example**
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76
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77 Filter the following file::
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78
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79 Chr Start End Ref Alt Func.refGene Gene.refGene ExonicFunc.refGene AAChange.refGene genomicSuperDups snp138 1000g2014oct_all esp6500si_all Strand context Chromosome Start_Position End_Position Reference_Allele Tumor_Seq_Allele2
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80 chr7 121717919 121717920 - G exonic AASS frameshift insertion AASS:NM_005763:exon23:c.2634dupC:p.A879fs NA rs147476318 NA NA - GCG chr7 121717919 121717920 - G
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81 chr1 230846235 230846235 T A exonic AGT nonsynonymous SNV AGT:NM_000029:exon2:c.A362T:p.H121L NA NA NA NA - GTG chr1 230846235 230846235 T A
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82 chr14 33290999 33290999 A G exonic AKAP6 nonsynonymous SNV AKAP6:NM_004274:exon13:c.A3980G:p.D1327G NA NA NA NA + GAC chr14 33290999 33290999 A G
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83 chr12 8082458 8082458 C T exonic SLC2A3 nonsynonymous SNV SLC2A3:NM_006931:exon6:c.G683A:p.R228Q NA rs200481428 0.000199681 NA - CCG chr12 8082458 8082458 C T
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84 chr4 70156391 70156391 T C exonic UGT2B28 nonsynonymous SNV UGT2B28:NM_053039:exon5:c.T1172C:p.V391A score=0.949699;Name=chr4:70035680 NA 0.000199681 NA + GTA chr4 70156391 70156391 T C
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85
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86 Will produce::
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87
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88 Chr Start End Ref Alt Func.refGene Gene.refGene ExonicFunc.refGene AAChange.refGene genomicSuperDups snp138 1000g2014oct_all esp6500si_all Strand context Chromosome Start_Position End_Position Reference_Allele Tumor_Seq_Allele2
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89 chr1 230846235 230846235 T A exonic AGT nonsynonymous SNV AGT:NM_000029:exon2:c.A362T:p.H121L NA NA NA NA - GTG chr1 230846235 230846235 T A
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90 chr14 33290999 33290999 A G exonic AKAP6 nonsynonymous SNV AKAP6:NM_004274:exon13:c.A3980G:p.D1327G NA NA NA NA + GAC chr14 33290999 33290999 A G
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91 chr4 70156391 70156391 T C exonic UGT2B28 nonsynonymous SNV UGT2B28:NM_053039:exon5:c.T1172C:p.V391A score=0.949699;Name=chr4:70035680 NA 0.000199681 NA + GTA chr4 70156391 70156391 T C
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92
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93
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94
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95 </help>
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96
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1
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97 <citations>
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98 <citation type="bibtex">
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99 @ARTICLE{ardin_mutspec:_2016,
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100 author = {Ardin et al},
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101 keywords = {Galaxy, Mutation signatures, Mutation spectra, Single base substitutions},
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102 title = {{MutSpec}: a Galaxy toolbox for streamlined analyses of somatic mutation spectra in human and mouse cancer genomes},
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103 url = {http://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-016-1011-z}
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104 }
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105 </citation>
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106 </citations>
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107
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0
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108 </tool>
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