Mercurial > repos > iuc > snpsift_dbnsfp

comparison snpSift_dbnsfp.xml @ 22:22ddfea1ecde draft

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author iuc
date Thu, 09 Apr 2015 22:47:00 -0400
parents 59f148f07bc5
children fc8a3e1e7880
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21:d7ed974243a4 22:22ddfea1ecde
1 <tool id="snpSift_dbnsfp_generic" name="SnpSift dbNSFP" version="4.0.0"> 1 <tool id="snpSift_dbnsfp" name="SnpSift dbNSFP" version="4.0.0">
2 <description>Add Annotations from dbNSFP and similar annotation DBs</description> 2 <description>Add Annotations from dbNSFP</description>
3 <expand macro="requirements" /> 3 <expand macro="requirements" />
4 <macros> 4 <macros>
5 <import>snpSift_macros.xml</import> 5 <import>snpSift_macros.xml</import>
6 </macros> 6 </macros>
7 <command> 7 <command>
28 <option value="history">dbNSFP database from your history</option> 28 <option value="history">dbNSFP database from your history</option>
29 </param> 29 </param>
30 <when value="cached"> 30 <when value="cached">
31 <param name="dbnsfp" type="select" label="Genome"> 31 <param name="dbnsfp" type="select" label="Genome">
32 <options from_data_table="snpsift_dbnsfp"> 32 <options from_data_table="snpsift_dbnsfp">
33 <column name="name" index="2"/> 33 <column name="name" index="1"/>
34 <column name="value" index="3"/> 34 <column name="value" index="2"/>
35 </options> 35 </options>
36 </param> 36 </param>
37 <param name="annotations" type="select" multiple="true" display="checkboxes" label="Annotate with"> 37 <param name="annotations" type="select" multiple="true" display="checkboxes" label="Annotate with">
38 <options from_data_table="snpsift_dbnsfp"> 38 <options from_data_table="snpsift_dbnsfp">
39 <column name="name" index="3"/> 39 <column name="name" index="3"/>
71 </test> 71 </test>
72 </tests> 72 </tests>
73 <help> 73 <help>
74 74
75 The dbNSFP is an integrated database of functional predictions from multiple algorithms (SIFT, Polyphen2, LRT and MutationTaster, PhyloP and GERP++, etc.). 75 The dbNSFP is an integrated database of functional predictions from multiple algorithms (SIFT, Polyphen2, LRT and MutationTaster, PhyloP and GERP++, etc.).
76 It contains variant annotations such as:
77 76
78 77
79 1000Gp1_AC 78 1000Gp1_AC
80 Alternative allele counts in the whole 1000 genomes phase 1 (1000Gp1) data 79 Alternative allele counts in the whole 1000 genomes phase 1 (1000Gp1) data
81 1000Gp1_AF 80 1000Gp1_AF
240 Uniprot ID number. Multiple entries separated by ";" 239 Uniprot ID number. Multiple entries separated by ";"
241 UniSNP_ids 240 UniSNP_ids
242 rs numbers from UniSNP, which is a cleaned version of dbSNP build 129, in format: rs number1;rs number2;... 241 rs numbers from UniSNP, which is a cleaned version of dbSNP build 129, in format: rs number1;rs number2;...
243 242
244 243
245 244 The website for dbNSFP database is https://sites.google.com/site/jpopgen/dbNSFP and there is only annotation for human hg18 and hg19 genome builds.
246 The procedure for preparing the dbNSFP data for use in SnpSift dbnsfp is in the SnpSift documentation: 245
247 http://snpeff.sourceforge.net/SnpSift.html#dbNSFP 246 However, any dbNSFP-like tabular file that be can used with SnpSift dbnsfp if it has::
248 247
249 A couple dbNSFP databases are prebuilt for SnpSift at: 248 - The first line of the file must be column headers that name the annotations.
250 http://sourceforge.net/projects/snpeff/files/databases/dbNSFP/ 249 - The first 4 columns are required and must be::
251 250 1. chromosome
252 251 2. position in chromosome
253 252 3. reference base
254 253 4. alternate base
255 **Uploading Your Own Annotations for any Genome**
256
257 The website for dbNSFP databases releases is:
258 https://sites.google.com/site/jpopgen/dbNSFP
259
260 But there is only annotation for human hg18, hg19, and hg38 genome builds.
261
262 However, any dbNSFP-like tabular file that be can used with SnpSift dbnsfp if it has:
263
264 - The first line of the file must be column headers that name the annotations.
265 - The first 4 columns are required and must be:
266
267 1. #chr - chromosome
268 2. pos(1-coor) - position in chromosome
269 3. ref - reference base
270 4. alt - alternate base
271
272 254
273 For example: 255 For example:
274 256
275 :: 257 ::
276 258
277 #chr pos(1-coor) ref alt aaref aaalt genename SIFT_score 259 #chr pos(1-coor) ref alt aaref aaalt genename SIFT_score
278 4 100239319 T A H L ADH1B 0 260 1 69134 A C E A OR4F5 0.03
279 4 100239319 T C H R ADH1B 0.15 261 1 69134 A G E G OR4F5 0.09
280 4 100239319 T G H P ADH1B 0 262 1 69134 A T E V OR4F5 0.03
281 263 4 100239319 T A H L ADH1B 0
282 264 4 100239319 T C H R ADH1B 0.15
283 The custom galaxy datatypes for dbNSFP can automatically convert the specially formatted tabular file for use by SnpSift dbNSFP: 265 4 100239319 T G H P ADH1B 0
284 1. Upload the tabular file, set the datatype as: **"dbnsfp.tabular"** 266
285 2. Edit the history dataset attributes (pencil icon): Use "Convert Format" to convert the **"dbnsfp.tabular"** to the correct format for SnpSift dbnsfp: **"snpsiftdbnsfp"**. 267
268 The uploaded tabular file should be set to datatype: "dbnsfp.tabular"
269 Using "Convert Format" the "dbnsfp.tabular" can be converted to the correct format for SnpSift dbnsfp.
286 270
287 The procedure for preparing the dbNSFP data for use in SnpSift dbnsfp is in the SnpSift documentation. 271 The procedure for preparing the dbNSFP data for use in SnpSift dbnsfp is in the SnpSift documentation.
288 272
289 273
290 @EXTERNAL_DOCUMENTATION@ 274 @EXTERNAL_DOCUMENTATION@