Mercurial > repos > jjohnson > snpeff
annotate snpSift_annotate.xml @ 5:8952990fcab9
Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases
| author | Jim Johnson <jj@umn.edu> |
|---|---|
| date | Wed, 27 Nov 2013 09:11:32 -0600 |
| parents | 6ad9205c1307 |
| children | 0ad9733e22a4 |
| rev | line source |
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Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases
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1 <tool id="snpSift_annotate" name="SnpSift Annotate" version="3.4"> |
| 0 | 2 <description>Annotate SNPs from dbSnp</description> |
| 3 <!-- | |
| 4 You will need to change the path to wherever your installation is. | |
| 5 You can change the amount of memory used, just change the -Xmx parameter (e.g. use -Xmx2G for 2Gb of memory) | |
| 6 --> | |
| 7 <requirements> | |
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Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases
Jim Johnson <jj@umn.edu>
parents:
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8 <requirement type="package" version="3.4">snpEff</requirement> |
| 0 | 9 </requirements> |
| 10 <command> | |
| 2 | 11 java -Xmx6G -jar \$SNPEFF_JAR_PATH/SnpSift.jar $annotate_cmd |
| 0 | 12 #if $annotate.id : |
| 13 -id | |
| 14 #elif $annotate.info_ids.__str__.strip() != '' : | |
| 15 -info "$annotate.info_ids" | |
| 16 #end if | |
| 17 -q $dbSnp $input > $output | |
| 18 </command> | |
| 19 <inputs> | |
| 20 <param format="vcf" name="input" type="data" label="VCF input"/> | |
| 21 <param format="vcf" name="dbSnp" type="data" label="VCF File with ID field annotated (e.g. dnSNP.vcf)" | |
| 22 help="The ID field for a variant in input will be assigned from a matching variant in this file."/> | |
| 23 <conditional name="annotate"> | |
| 24 <param name="id" type="boolean" truevalue="id" falsevalue="info" checked="True" label="Only annotate ID field (do not add INFO field)" help=""/> | |
| 25 <when value="id"/> | |
| 26 <when value="info"> | |
|
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Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases
Jim Johnson <jj@umn.edu>
parents:
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changeset
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27 <param name="info_ids" type="text" value="" size="60" optional="true" label="Limit INFO annotation to these INFO IDs" |
| 0 | 28 help="list is a comma separated list of fields. When blank, all INFO fields are included"> |
| 29 <validator type="regex" message="IDs separted by commas">^(([a-zA-Z][a-zA-Z0-9_-]*)(,[a-zA-Z][a-zA-Z0-9_-]*)*)?$</validator> | |
| 30 </param> | |
| 31 </when> | |
| 32 </conditional> | |
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33 <param name="annotate_cmd" type="boolean" truevalue="annMem" falsevalue="annotate" checked="false" label="Annotate in Memory"> |
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34 <help> |
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Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases
Jim Johnson <jj@umn.edu>
parents:
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35 Allows unsorted VCF files, but it loads 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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parents:
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37 </help> |
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parents:
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38 </param> |
| 0 | 39 </inputs> |
| 40 <stdio> | |
| 41 <exit_code range=":-1" level="fatal" description="Error: Cannot open file" /> | |
| 42 <exit_code range="1:" level="fatal" description="Error" /> | |
| 43 </stdio> | |
| 44 | |
| 45 <outputs> | |
| 46 <data format="vcf" name="output" /> | |
| 47 </outputs> | |
| 48 <tests> | |
| 49 <test> | |
| 50 <param name="input" ftype="vcf" value="annotate_1.vcf"/> | |
| 51 <param name="dbSnp" ftype="vcf" value="db_test_1.vcf"/> | |
| 52 <param name="annotate_cmd" value="False"/> | |
| 53 <param name="id" value="True"/> | |
| 54 <output name="output"> | |
| 55 <assert_contents> | |
| 56 <has_text text="rs76166080" /> | |
| 57 </assert_contents> | |
| 58 </output> | |
| 59 </test> | |
| 60 </tests> | |
| 61 <help> | |
| 62 | |
| 63 This is typically used to annotate IDs from dbSnp. | |
| 64 | |
| 65 For details about this tool, please go to http://snpeff.sourceforge.net/SnpSift.html#annotate | |
| 66 | |
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67 Annotatating only the ID field from dbSnp137.vcf :: |
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68 |
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parents:
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69 Input 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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parents:
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72 22 16346045 . T C 0.0 FAIL NS=244 |
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parents:
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73 22 16350245 . C A 0.0 FAIL NS=192 |
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74 |
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75 Annotated Output VCF: |
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parents:
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76 #CHROM POS ID REF ALT QUAL FILTER INFO |
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parents:
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77 22 16157571 . T G 0.0 FAIL NS=53 |
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parents:
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78 22 16346045 rs56234788 T C 0.0 FAIL NS=244 |
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parents:
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79 22 16350245 rs2905295 C A 0.0 FAIL NS=192 |
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parents:
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80 |
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81 |
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82 |
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Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases
Jim Johnson <jj@umn.edu>
parents:
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83 Annotatating both the ID and INFO fields from dbSnp137.vcf :: |
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Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases
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parents:
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84 |
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parents:
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85 Input VCF: |
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Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases
Jim Johnson <jj@umn.edu>
parents:
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86 #CHROM POS ID REF ALT QUAL FILTER INFO |
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parents:
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87 22 16157571 . T G 0.0 FAIL NS=53 |
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8952990fcab9
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parents:
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88 22 16346045 . T C 0.0 FAIL NS=244 |
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parents:
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89 22 16350245 . C A 0.0 FAIL NS=192 |
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parents:
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90 |
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91 Annotated Output VCF: |
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Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases
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parents:
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92 #CHROM POS ID REF ALT QUAL FILTER INFO |
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parents:
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93 22 16157571 . T G 0.0 FAIL NS=53 |
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parents:
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94 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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Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases
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parents:
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95 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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parents:
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96 |
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97 |
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98 SnpEff citation: |
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99 "A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3.", Cingolani P, Platts A, Wang le L, Coon M, Nguyen T, Wang L, Land SJ, Lu X, Ruden DM. Fly (Austin). 2012 Apr-Jun;6(2):80-92. PMID: 22728672 [PubMed - in process] |
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parents:
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100 |
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101 SnpSift citation: |
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parents:
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102 "Using Drosophila melanogaster as a model for genotoxic chemical mutational studies with a new program, SnpSift", Cingolani, P., et. al., Frontiers in Genetics, 3, 2012. |
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parents:
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103 |
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104 |
| 0 | 105 </help> |
| 106 </tool> | |
| 107 |