Mercurial > repos > jjohnson > snpeff
annotate snpSift_annotate.xml @ 7:0ad9733e22a4
Uploaded
| author | bgruening |
|---|---|
| date | Fri, 29 Nov 2013 09:27:22 -0500 |
| parents | 8952990fcab9 |
| children |
| rev | line source |
|---|---|
|
5
8952990fcab9
Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases
Jim Johnson <jj@umn.edu>
parents:
2
diff
changeset
|
1 <tool id="snpSift_annotate" name="SnpSift Annotate" version="3.4"> |
| 7 | 2 <description>SNPs from dbSnp</description> |
| 3 <!-- | |
| 4 You can change the amount of memory used, just change the -Xmx parameter (e.g. use -Xmx2G for 2Gb of memory) | |
| 5 --> | |
| 6 <expand macro="requirements" /> | |
| 7 <macros> | |
| 8 <import>snpEff_macros.xml</import> | |
| 9 </macros> | |
| 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 > $output | |
| 7 | 18 </command> |
| 19 <inputs> | |
| 20 <param format="vcf" name="input" type="data" label="Variant input file in VCF format"/> | |
| 21 <param format="vcf" name="dbSnp" type="data" label="VCF File with ID field annotated (e.g. dnSNP.vcf)" | |
| 22 help="The ID field for a variant in input will be assigned from a matching variant in this file."/> | |
| 23 <conditional name="annotate"> | |
| 24 <param name="id" type="boolean" truevalue="id" falsevalue="info" checked="True" label="Only annotate ID field (do not add INFO field)" help=""/> | |
| 25 <when value="id"/> | |
| 26 <when value="info"> | |
| 27 <param name="info_ids" type="text" value="" size="60" optional="true" label="Limit INFO annotation to these INFO IDs" | |
| 28 help="list is a comma separated list of fields. When blank, all INFO fields are included"> | |
| 29 <validator type="regex" message="IDs separted by commas">^(([a-zA-Z][a-zA-Z0-9_-]*)(,[a-zA-Z][a-zA-Z0-9_-]*)*)?$</validator> | |
|
5
8952990fcab9
Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases
Jim Johnson <jj@umn.edu>
parents:
2
diff
changeset
|
30 </param> |
| 7 | 31 </when> |
| 32 </conditional> | |
| 33 <param name="annotate_cmd" type="boolean" truevalue="annMem" falsevalue="annotate" checked="false" label="Allow unsorted VCF files"> | |
| 34 <help> | |
| 35 This option will load the entire 'database' VCF file into memory (which may not be practical for large 'database' VCF files). | |
| 36 Otherwise, both the database and the input VCF files should be sorted by position (Chromosome sort order can differ between files). | |
| 37 </help> | |
| 38 </param> | |
| 39 </inputs> | |
| 40 <expand macro="stdio" /> | |
| 41 <outputs> | |
| 42 <data format="vcf" name="output" /> | |
| 43 </outputs> | |
| 44 <tests> | |
| 45 <test> | |
| 46 <param name="input" ftype="vcf" value="annotate_1.vcf"/> | |
| 47 <param name="dbSnp" ftype="vcf" value="db_test_1.vcf"/> | |
| 48 <param name="annotate_cmd" value="False"/> | |
| 49 <param name="id" value="True"/> | |
| 50 <output name="output"> | |
| 51 <assert_contents> | |
| 52 <has_text text="rs76166080" /> | |
| 53 </assert_contents> | |
| 54 </output> | |
| 55 </test> | |
| 56 </tests> | |
| 57 <help> | |
| 0 | 58 |
| 59 This is typically used to annotate IDs from dbSnp. | |
| 60 | |
|
5
8952990fcab9
Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases
Jim Johnson <jj@umn.edu>
parents:
2
diff
changeset
|
61 Annotatating only the ID field from dbSnp137.vcf :: |
|
8952990fcab9
Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases
Jim Johnson <jj@umn.edu>
parents:
2
diff
changeset
|
62 |
|
8952990fcab9
Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases
Jim Johnson <jj@umn.edu>
parents:
2
diff
changeset
|
63 Input VCF: |
|
8952990fcab9
Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases
Jim Johnson <jj@umn.edu>
parents:
2
diff
changeset
|
64 CHROM POS ID REF ALT QUAL FILTER INFO |
|
8952990fcab9
Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases
Jim Johnson <jj@umn.edu>
parents:
2
diff
changeset
|
65 22 16157571 . T G 0.0 FAIL NS=53 |
|
8952990fcab9
Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases
Jim Johnson <jj@umn.edu>
parents:
2
diff
changeset
|
66 22 16346045 . T C 0.0 FAIL NS=244 |
|
8952990fcab9
Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases
Jim Johnson <jj@umn.edu>
parents:
2
diff
changeset
|
67 22 16350245 . C A 0.0 FAIL NS=192 |
|
8952990fcab9
Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases
Jim Johnson <jj@umn.edu>
parents:
2
diff
changeset
|
68 |
|
8952990fcab9
Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases
Jim Johnson <jj@umn.edu>
parents:
2
diff
changeset
|
69 Annotated Output VCF: |
|
8952990fcab9
Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases
Jim Johnson <jj@umn.edu>
parents:
2
diff
changeset
|
70 #CHROM POS ID REF ALT QUAL FILTER INFO |
|
8952990fcab9
Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases
Jim Johnson <jj@umn.edu>
parents:
2
diff
changeset
|
71 22 16157571 . T G 0.0 FAIL NS=53 |
|
8952990fcab9
Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases
Jim Johnson <jj@umn.edu>
parents:
2
diff
changeset
|
72 22 16346045 rs56234788 T C 0.0 FAIL NS=244 |
|
8952990fcab9
Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases
Jim Johnson <jj@umn.edu>
parents:
2
diff
changeset
|
73 22 16350245 rs2905295 C A 0.0 FAIL NS=192 |
|
8952990fcab9
Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases
Jim Johnson <jj@umn.edu>
parents:
2
diff
changeset
|
74 |
|
8952990fcab9
Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases
Jim Johnson <jj@umn.edu>
parents:
2
diff
changeset
|
75 |
|
8952990fcab9
Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases
Jim Johnson <jj@umn.edu>
parents:
2
diff
changeset
|
76 |
|
8952990fcab9
Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases
Jim Johnson <jj@umn.edu>
parents:
2
diff
changeset
|
77 Annotatating both the ID and INFO fields from dbSnp137.vcf :: |
|
8952990fcab9
Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases
Jim Johnson <jj@umn.edu>
parents:
2
diff
changeset
|
78 |
|
8952990fcab9
Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases
Jim Johnson <jj@umn.edu>
parents:
2
diff
changeset
|
79 Input VCF: |
|
8952990fcab9
Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases
Jim Johnson <jj@umn.edu>
parents:
2
diff
changeset
|
80 #CHROM POS ID REF ALT QUAL FILTER INFO |
|
8952990fcab9
Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases
Jim Johnson <jj@umn.edu>
parents:
2
diff
changeset
|
81 22 16157571 . T G 0.0 FAIL NS=53 |
|
8952990fcab9
Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases
Jim Johnson <jj@umn.edu>
parents:
2
diff
changeset
|
82 22 16346045 . T C 0.0 FAIL NS=244 |
|
8952990fcab9
Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases
Jim Johnson <jj@umn.edu>
parents:
2
diff
changeset
|
83 22 16350245 . C A 0.0 FAIL NS=192 |
|
8952990fcab9
Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases
Jim Johnson <jj@umn.edu>
parents:
2
diff
changeset
|
84 |
|
8952990fcab9
Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases
Jim Johnson <jj@umn.edu>
parents:
2
diff
changeset
|
85 Annotated Output VCF: |
|
8952990fcab9
Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases
Jim Johnson <jj@umn.edu>
parents:
2
diff
changeset
|
86 #CHROM POS ID REF ALT QUAL FILTER INFO |
|
8952990fcab9
Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases
Jim Johnson <jj@umn.edu>
parents:
2
diff
changeset
|
87 22 16157571 . T G 0.0 FAIL NS=53 |
|
8952990fcab9
Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases
Jim Johnson <jj@umn.edu>
parents:
2
diff
changeset
|
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 |
|
8952990fcab9
Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases
Jim Johnson <jj@umn.edu>
parents:
2
diff
changeset
|
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 |
|
8952990fcab9
Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases
Jim Johnson <jj@umn.edu>
parents:
2
diff
changeset
|
90 |
|
8952990fcab9
Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases
Jim Johnson <jj@umn.edu>
parents:
2
diff
changeset
|
91 |
| 7 | 92 @EXTERNAL_DOCUMENTATION@ |
|
5
8952990fcab9
Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases
Jim Johnson <jj@umn.edu>
parents:
2
diff
changeset
|
93 |
| 7 | 94 @CITATION_SECTION@ |
|
5
8952990fcab9
Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases
Jim Johnson <jj@umn.edu>
parents:
2
diff
changeset
|
95 |
|
8952990fcab9
Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases
Jim Johnson <jj@umn.edu>
parents:
2
diff
changeset
|
96 |
| 7 | 97 </help> |
| 0 | 98 </tool> |
| 99 |