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1 <tool id="snpSift_annotate" name="SnpSift Annotate" version="3.6">
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2 <description>SNPs from dbSnp</description>
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3 <!--
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4 You can change the amount of memory used, just change the -Xmx parameter (e.g. use -Xmx2G for 2Gb of memory)
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5 -->
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6 <expand macro="requirements" />
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7 <macros>
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8 <import>snpEff_macros.xml</import>
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9 </macros>
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10 <command>
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11 java -Xmx6G -jar \$SNPEFF_JAR_PATH/SnpSift.jar $annotate_cmd
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12 #if $annotate.id :
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13 -id
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14 #elif $annotate.info_ids.__str__.strip() != '' :
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15 -info "$annotate.info_ids"
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16 #end if
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17 -q $dbSnp $input > $output
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18 </command>
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19 <inputs>
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20 <param format="vcf" name="input" type="data" label="Variant input file in VCF format"/>
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21 <param format="vcf" name="dbSnp" type="data" label="VCF File with ID field annotated (e.g. dnSNP.vcf)"
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22 help="The ID field for a variant in input will be assigned from a matching variant in this file."/>
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23 <conditional name="annotate">
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24 <param name="id" type="boolean" truevalue="id" falsevalue="info" checked="True" label="Only annotate ID field (do not add INFO field)" help=""/>
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25 <when value="id"/>
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26 <when value="info">
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27 <param name="info_ids" type="text" value="" size="60" optional="true" label="Limit INFO annotation to these INFO IDs"
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28 help="list is a comma separated list of fields. When blank, all INFO fields are included">
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29 <validator type="regex" message="IDs separted by commas">^(([a-zA-Z][a-zA-Z0-9_-]*)(,[a-zA-Z][a-zA-Z0-9_-]*)*)?$</validator>
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30 </param>
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31 </when>
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32 </conditional>
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33 <param name="annotate_cmd" type="boolean" truevalue="annMem" falsevalue="annotate" checked="false" label="Allow unsorted VCF files">
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34 <help>
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35 This option will load the entire 'database' VCF file into memory (which may not be practical for large 'database' VCF files).
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36 Otherwise, both the database and the input VCF files should be sorted by position (Chromosome sort order can differ between files).
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37 </help>
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38 </param>
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39 </inputs>
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40 <expand macro="stdio" />
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41 <outputs>
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42 <data format="vcf" name="output" />
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43 </outputs>
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44 <tests>
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45 <test>
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46 <param name="input" ftype="vcf" value="annotate_1.vcf"/>
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47 <param name="dbSnp" ftype="vcf" value="db_test_1.vcf"/>
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48 <param name="annotate_cmd" value="False"/>
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49 <param name="id" value="True"/>
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50 <output name="output">
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51 <assert_contents>
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52 <has_text text="rs76166080" />
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53 </assert_contents>
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54 </output>
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55 </test>
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56 </tests>
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57 <help>
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58
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59 This is typically used to annotate IDs from dbSnp.
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60
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61 Annotatating only the ID field from dbSnp137.vcf ::
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62
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63 Input VCF:
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64 CHROM POS ID REF ALT QUAL FILTER INFO
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65 22 16157571 . T G 0.0 FAIL NS=53
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66 22 16346045 . T C 0.0 FAIL NS=244
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67 22 16350245 . C A 0.0 FAIL NS=192
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68
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69 Annotated Output VCF:
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70 #CHROM POS ID REF ALT QUAL FILTER INFO
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71 22 16157571 . T G 0.0 FAIL NS=53
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72 22 16346045 rs56234788 T C 0.0 FAIL NS=244
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73 22 16350245 rs2905295 C A 0.0 FAIL NS=192
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74
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75
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76
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77 Annotatating both the ID and INFO fields from dbSnp137.vcf ::
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78
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79 Input VCF:
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80 #CHROM POS ID REF ALT QUAL FILTER INFO
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81 22 16157571 . T G 0.0 FAIL NS=53
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82 22 16346045 . T C 0.0 FAIL NS=244
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83 22 16350245 . C A 0.0 FAIL NS=192
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84
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85 Annotated Output VCF:
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86 #CHROM POS ID REF ALT QUAL FILTER INFO
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87 22 16157571 . T G 0.0 FAIL NS=53
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88 22 16346045 rs56234788 T C 0.0 FAIL NS=244;RSPOS=16346045;GMAF=0.162248628884826;dbSNPBuildID=129;SSR=0;SAO=0;VP=050100000000000100000100;WGT=0;VC=SNV;SLO;GNO
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89 22 16350245 rs2905295 C A 0.0 FAIL NS=192;RSPOS=16350245;GMAF=0.230804387568556;dbSNPBuildID=101;SSR=1;SAO=0;VP=050000000000000100000140;WGT=0;VC=SNV;GNO
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90
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91
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92 @EXTERNAL_DOCUMENTATION@
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93 http://snpeff.sourceforge.net/SnpSift.html#annotate
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94
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95 @CITATION_SECTION@
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96
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97
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98 </help>
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99 </tool>
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100
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