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comparison snpSift_dbnsfp.xml @ 0:6e5ba121e250 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp_generic/ commit d12355cea76843e3ed6f09d96c3e9fe22afe4a4f
author iuc
date Mon, 05 Dec 2016 12:05:54 -0500
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1 <tool id="snpSift_dbnsfp_generic" name="SnpSift dbNSFP" version="@WRAPPER_VERSION@.1">
2 <description>Add Annotations from dbNSFP and similar annotation DBs</description>
3 <macros>
4 <import>snpSift_macros.xml</import>
5 </macros>
6 <expand macro="requirements" />
7 <expand macro="stdio" />
8 <expand macro="version_command" />
9 <command><![CDATA[
10 @CONDA_SNPSIFT_JAR_PATH@ &&
11 java -Xmx6G -jar "\$SNPSIFT_JAR_PATH/SnpSift.jar" dbnsfp -v
12 #if $db.dbsrc == 'cached':
13 -db $db.dbnsfp
14 #if $db.annotations and str($db.annotations) != '':
15 -f "$db.annotations"
16 #end if
17 #else:
18 -db "${db.dbnsfpdb.extra_files_path}/${db.dbnsfpdb.metadata.bgzip}"
19 #if $db.annotations and str($db.annotations) != '':
20 -f "$db.annotations"
21 #end if
22 #end if
23 "$input" > "$output"
24 2> tmp.err && grep -v file tmp.err
25 ]]>
26 </command>
27 <inputs>
28 <param name="input" type="data" format="vcf" label="Variant input file in VCF format"/>
29 <conditional name="db">
30 <param name="dbsrc" type="select" label="dbNSFP ">
31 <option value="cached">Locally installed dbNSFP database </option>
32 <option value="history">dbNSFP database from your history</option>
33 </param>
34 <when value="cached">
35 <param name="dbnsfp" type="select" label="Genome">
36 <options from_data_table="snpsift_dbnsfp">
37 <column name="name" index="2"/>
38 <column name="value" index="3"/>
39 </options>
40 </param>
41 <param name="annotations" type="select" multiple="true" display="checkboxes" label="Annotate with">
42 <options from_data_table="snpsift_dbnsfp">
43 <column name="name" index="3"/>
44 <column name="value" index="3"/>
45 <filter type="param_value" ref="dbnsfp" column="2" />
46 <filter type="multiple_splitter" column="3" separator=","/>
47 </options>
48 </param>
49 </when>
50 <when value="history">
51 <param name="dbnsfpdb" type="data" format="snpsiftdbnsfp" label="DbNSFP"/>
52 <param name="annotations" type="select" multiple="true" display="checkboxes" label="Annotate with">
53 <options>
54 <filter type="data_meta" ref="dbnsfpdb" key="annotation" />
55 </options>
56 </param>
57 </when>
58 </conditional>
59 </inputs>
60 <outputs>
61 <data format="vcf" name="output" />
62 </outputs>
63 <tests>
64 <!-- This cannot be tested at the moment because test_dbnsfpdb.tabular
65 is converted from dbnsfp.tabular to snpsiftdbnsfp format on-the-fly
66 when this tool is run and annotation metadata is not available
67 until after the conversion is completed.
68 <test>
69 <param name="input" ftype="vcf" value="test_annotate_in.vcf"/>
70 <param name="dbsrc" value="history"/>
71 <param name="dbnsfpdb" value="test_dbnsfpdb.tabular" ftype="dbnsfp.tabular" />
72 <param name="annotations" value="aaref,aaalt,genename,aapos,SIFT_score"/>
73 <output name="output">
74 <assert_contents>
75 <has_text text="dbNSFP_SIFT_score=0.15" />
76 </assert_contents>
77 </output>
78 </test> -->
79 </tests>
80 <help><![CDATA[
81
82 The dbNSFP is an integrated database of functional predictions from multiple algorithms (SIFT, Polyphen2, LRT and MutationTaster, PhyloP and GERP++, etc.).
83 It contains variant annotations such as:
84
85
86 1000Gp1_AC
87 Alternative allele counts in the whole 1000 genomes phase 1 (1000Gp1) data
88 1000Gp1_AF
89 Alternative allele frequency in the whole 1000Gp1 data
90 1000Gp1_AFR_AC
91 Alternative allele counts in the 1000Gp1 African descendent samples
92 1000Gp1_AFR_AF
93 Alternative allele frequency in the 1000Gp1 African descendent samples
94 1000Gp1_AMR_AC
95 Alternative allele counts in the 1000Gp1 American descendent samples
96 1000Gp1_AMR_AF
97 Alternative allele frequency in the 1000Gp1 American descendent samples
98 1000Gp1_ASN_AC
99 Alternative allele counts in the 1000Gp1 Asian descendent samples
100 1000Gp1_ASN_AF
101 Alternative allele frequency in the 1000Gp1 Asian descendent samples
102 1000Gp1_EUR_AC
103 Alternative allele counts in the 1000Gp1 European descendent samples
104 1000Gp1_EUR_AF
105 Alternative allele frequency in the 1000Gp1 European descendent samples
106 aaalt
107 Alternative amino acid. "." if the variant is a splicing site SNP (2bp on each end of an intron)
108 aapos
109 Amino acid position as to the protein. "-1" if the variant is a splicing site SNP (2bp on each end of an intron)
110 aapos_SIFT
111 ENSP id and amino acid positions corresponding to SIFT scores. Multiple entries separated by ";"
112 aapos_FATHMM
113 ENSP id and amino acid positions corresponding to FATHMM scores. Multiple entries separated by ";"
114 aaref
115 Reference amino acid. "." if the variant is a splicing site SNP (2bp on each end of an intron)
116 alt
117 Alternative nucleotide allele (as on the + strand)
118 Ancestral_allele
119 Ancestral allele (based on 1000 genomes reference data)
120 cds_strand
121 Coding sequence (CDS) strand (+ or -)
122 chr
123 Chromosome number
124 codonpos
125 Position on the codon (1, 2 or 3)
126 Ensembl_geneid
127 Ensembl gene ID
128 Ensembl_transcriptid
129 Ensembl transcript IDs (separated by ";")
130 ESP6500_AA_AF
131 Alternative allele frequency in the African American samples of the NHLBI GO Exome Sequencing Project (ESP6500 data set)
132 ESP6500_EA_AF
133 Alternative allele frequency in the European American samples of the NHLBI GO Exome Sequencing Project (ESP6500 data set)
134 FATHMM_pred
135 If a FATHMM_score is <=-1.5 (or rankscore <=0.81415) the corresponding non-synonymous SNP is predicted as "D(AMAGING)"; otherwise it is predicted as "T(OLERATED)". Multiple predictions separated by ";"
136 FATHMM_rankscore
137 FATHMMori scores were ranked among all FATHMMori scores in dbNSFP. The rankscore is the ratio of the rank of the score over the total number of FATHMMori scores in dbNSFP. If there are multiple scores, only the most damaging (largest) rankscore is presented. The scores range from 0 to 1
138 FATHMM_score
139 FATHMM default score (FATHMMori)
140 fold-degenerate
141 Degenerate type (0, 2 or 3)
142 genename
143 Gene name; if the non-synonymous SNP can be assigned to multiple genes, gene names are separated by ";"
144 GERP++_NR
145 GERP++ neutral rate
146 GERP++_RS
147 GERP++ RS score, the larger the score, the more conserved the site
148 GERP++_RS_rankscore
149 GERP++ RS scores were ranked among all GERP++ RS scores in dbNSFP. The rankscore is the ratio of the rank of the score over the total number of GERP++ RS scores in dbNSFP
150 hg18_pos(1-coor)
151 Physical position on the chromosome as to hg18 (1-based coordinate)
152 Interpro_domain
153 Domain or conserved site on which the variant locates
154 LR_pred
155 Prediction of our LR based ensemble prediction score, "T(olerated)" or "D(amaging)". The score cutoff between "D" and "T" is 0.5. The rankscore cutoff between "D" and "T" is 0.82268
156 LR_rankscore
157 LR scores were ranked among all LR scores in dbNSFP. The rankscore is the ratio of the rank of the score over the total number of LR scores in dbNSFP. The scores range from 0 to 1
158 LR_score
159 Our logistic regression (LR) based ensemble prediction score, which incorporated 10 scores (SIFT, PolyPhen-2 HDIV, PolyPhen-2 HVAR, GERP++, MutationTaster, Mutation Assessor, FATHMM, LRT, SiPhy, PhyloP) and the maximum frequency observed in the 1000 genomes populations. Larger value means the SNV is more likely to be damaging. Scores range from 0 to 1
160 LRT_Omega
161 Estimated nonsynonymous-to-synonymous-rate ratio (Omega, reported by LRT)
162 LRT_converted_rankscore
163 LRTori scores were first converted as LRTnew=1-LRTori*0.5 if Omega<1, or LRTnew=LRTori*0.5 if Omega>=1. Then LRTnew scores were ranked among all LRTnew scores in dbNSFP. The rankscore is the ratio of the rank over the total number of the scores in dbNSFP. The scores range from 0.00166 to 0.85682
164 LRT_pred
165 LRT prediction, D(eleterious), N(eutral) or U(nknown), which is not solely determined by the score
166 LRT_score
167 The original LRT two-sided p-value (LRTori), ranges from 0 to 1
168 MutationAssessor_pred
169 MutationAssessor's functional impact of a variant
170 MutationAssessor_rankscore
171 MAori scores were ranked among all MAori scores in dbNSFP. The rankscore is the ratio of the rank of the score over the total number of MAori scores in dbNSFP. The scores range from 0 to 1
172 MutationAssessor_score
173 MutationAssessor functional impact combined score (MAori)
174 MutationTaster_converted_rankscore
175 The MTori scores were first converted: if the prediction is "A" or "D" MTnew=MTori; if the prediction is "N" or "P", MTnew=1-MTori. Then MTnew scores were ranked among all MTnew scores in dbNSFP. The rankscore is the ratio of the rank of the score over the total number of MTnew scores in dbNSFP. The scores range from 0.0931 to 0.80722
176 MutationTaster_pred
177 MutationTaster prediction
178 MutationTaster_score
179 MutationTaster p-value (MTori), ranges from 0 to 1
180 phastCons46way_placental
181 phastCons conservation score based on the multiple alignments of 33 placental mammal genomes (including human). The larger the score, the more conserved the site
182 phastCons46way_placental_rankscore
183 phastCons46way_placental scores were ranked among all phastCons46way_placental scores in dbNSFP. The rankscore is the ratio of the rank of the score over the total number of phastCons46way_placental scores in dbNSFP
184 phastCons46way_primate
185 phastCons conservation score based on the multiple alignments of 10 primate genomes (including human). The larger the score, the more conserved the site
186 phastCons46way_primate_rankscore
187 phastCons46way_primate scores were ranked among all phastCons46way_primate scores in dbNSFP. The rankscore is the ratio of the rank of the score over the total number of phastCons46way_primate scores in dbNSFP
188 phastCons100way_vertebrate
189 phastCons conservation score based on the multiple alignments of 100 vertebrate genomes (including human). The larger the score, the more conserved the site
190 phastCons100way_vertebrate_rankscore
191 phastCons100way_vertebrate scores were ranked among all phastCons100way_vertebrate scores in dbNSFP. The rankscore is the ratio of the rank of the score over the total number of phastCons100way_vertebrate scores in dbNSFP
192 phyloP46way_placental
193 phyloP (phylogenetic p-values) conservation score based on the multiple alignments of 33 placental mammal genomes (including human). The larger the score, the more conserved the site
194 phyloP46way_placental_rankscore
195 phyloP46way_placental scores were ranked among all phyloP46way_placental scores in dbNSFP. The rankscore is the ratio of the rank of the score over the total number of phyloP46way_placental scores in dbNSFP
196 phyloP46way_primate
197 phyloP (phylogenetic p-values) conservation score based on the multiple alignments of 10 primate genomes (including human). The larger the score, the more conserved the site
198 phyloP46way_primate_rankscore
199 phyloP46way_primate scores were ranked among all phyloP46way_primate scores in dbNSFP. The rankscore is the ratio of the rank of the score over the total number of phyloP46way_primate scores in dbNSFP
200 phyloP100way_vertebrate
201 phyloP (phylogenetic p-values) conservation score based on the multiple alignments of 100 vertebrate genomes (including human). The larger the score, the more conserved the site
202 phyloP100way_vertebrate_rankscore
203 phyloP100way_vertebrate scores were ranked among all phyloP100way_vertebrate scores in dbNSFP. The rankscore is the ratio of the rank of the score over the total number of phyloP100way_vertebrate scores in dbNSFP
204 Polyphen2_HDIV_pred
205 Polyphen2 prediction based on HumDiv
206 Polyphen2_HDIV_rankscore
207 Polyphen2 HDIV scores were first ranked among all HDIV scores in dbNSFP. The rankscore is the ratio of the rank the score over the total number of the scores in dbNSFP. If there are multiple scores, only the most damaging (largest) rankscore is presented. The scores range from 0.02656 to 0.89917
208 Polyphen2_HDIV_score
209 Polyphen2 score based on HumDiv, i.e. hdiv_prob. The score ranges from 0 to 1. Multiple entries separated by ";"
210 Polyphen2_HVAR_pred
211 Polyphen2 prediction based on HumVar
212 Polyphen2_HVAR_rankscore
213 Polyphen2 HVAR scores were first ranked among all HVAR scores in dbNSFP. The rankscore is the ratio of the rank the score over the total number of the scores in dbNSFP. If there are multiple scores, only the most damaging (largest) rankscore is presented. The scores range from 0.01281 to 0.9711
214 Polyphen2_HVAR_score
215 Polyphen2 score based on HumVar, i.e. hvar_prob. The score ranges from 0 to 1. Multiple entries separated by ";"
216 pos(1-coor)
217 Physical position on the chromosome as to hg19 (1-based coordinate)
218 RadialSVM_pred
219 Prediction of our SVM based ensemble prediction score, "T(olerated)" or "D(amaging)". The score cutoff between "D" and "T" is 0. The rankscore cutoff between "D" and "T" is 0.83357
220 RadialSVM_rankscore
221 RadialSVM scores were ranked among all RadialSVM scores in dbNSFP. The rankscore is the ratio of the rank of the screo over the total number of RadialSVM scores in dbNSFP. The scores range from 0 to 1
222 RadialSVM_score
223 Our support vector machine (SVM) based ensemble prediction score, which incorporated 10 scores (SIFT, PolyPhen-2 HDIV, PolyPhen-2 HVAR, GERP++, MutationTaster, Mutation Assessor, FATHMM, LRT, SiPhy, PhyloP) and the maximum frequency observed in the 1000 genomes populations. Larger value means the SNV is more likely to be damaging. Scores range from -2 to 3 in dbNSFP
224 ref
225 Reference nucleotide allele (as on the + strand)
226 refcodon
227 Reference codon
228 Reliability_index
229 Number of observed component scores (except the maximum frequency in the 1000 genomes populations) for RadialSVM and LR. Ranges from 1 to 10. As RadialSVM and LR scores are calculated based on imputed data, the less missing component scores, the higher the reliability of the scores and predictions
230 SIFT_converted_rankscore
231 SIFTori scores were first converted to SIFTnew=1-SIFTori, then ranked among all SIFTnew scores in dbNSFP. The rankscore is the ratio of the rank the SIFTnew score over the total number of SIFTnew scores in dbNSFP. If there are multiple scores, only the most damaging (largest) rankscore is presented. The rankscores range from 0.02654 to 0.87932
232 SIFT_pred
233 If SIFTori is smaller than 0.05 (rankscore>0.55) the corresponding non-synonymous SNP is predicted as "D(amaging)"; otherwise it is predicted as "T(olerated)". Multiple predictions separated by ";"
234 SIFT_score
235 SIFT score (SIFTori). Scores range from 0 to 1. The smaller the score the more likely the SNP has damaging effect. Multiple scores separated by ";"
236 SiPhy_29way_logOdds
237 SiPhy score based on 29 mammals genomes. The larger the score, the more conserved the site
238 SiPhy_29way_pi
239 The estimated stationary distribution of A, C, G and T at the site, using SiPhy algorithm based on 29 mammals genomes
240 SLR_test_statistic
241 SLR test statistic for testing natural selection on codons. A negative value indicates negative selection, and a positive value indicates positive selection. Larger magnitude of the value suggests stronger evidence
242 Uniprot_aapos
243 Amino acid position as to Uniprot. Multiple entries separated by ";"
244 Uniprot_acc
245 Uniprot accession number. Multiple entries separated by ";"
246 Uniprot_id
247 Uniprot ID number. Multiple entries separated by ";"
248 UniSNP_ids
249 rs numbers from UniSNP, which is a cleaned version of dbSNP build 129, in format: rs number1;rs number2;...
250
251
252 The procedure for preparing the dbNSFP data for use in SnpSift dbnsfp and a couple of prebuilt dbNSFP databases are available at:
253 http://snpeff.sourceforge.net/SnpSift.html#dbNSFP
254
255
256 **Uploading Your Own Annotations for any Genome**
257
258 The website for dbNSFP databases releases is:
259 https://sites.google.com/site/jpopgen/dbNSFP
260
261 But there is only annotation for human hg18, hg19, and hg38 genome builds.
262
263 However, any dbNSFP-like tabular file that be can used with SnpSift dbnsfp if it has:
264
265 - The first line of the file must be column headers that name the annotations.
266 - The first 4 columns are required and must be:
267
268 1. #chr - chromosome
269 2. pos(1-coor) - position in chromosome
270 3. ref - reference base
271 4. alt - alternate base
272
273
274 For example:
275
276 ::
277
278 #chr pos(1-coor) ref alt aaref aaalt genename SIFT_score
279 4 100239319 T A H L ADH1B 0
280 4 100239319 T C H R ADH1B 0.15
281 4 100239319 T G H P ADH1B 0
282
283
284 The custom galaxy datatypes for dbNSFP can automatically convert the specially formatted tabular file for use by SnpSift dbNSFP:
285 1. Upload the tabular file, set the datatype as: **"dbnsfp.tabular"**
286 2. Edit the history dataset attributes (pencil icon): Use "Convert Format" to convert the **"dbnsfp.tabular"** to the correct format for SnpSift dbnsfp: **"snpsiftdbnsfp"**.
287
288 The procedure for preparing the dbNSFP data for use in SnpSift dbnsfp is in the SnpSift documentation.
289
290
291 @EXTERNAL_DOCUMENTATION@
292 http://snpeff.sourceforge.net/SnpSift.html#dbNSFP
293 ]]>
294 </help>
295 <expand macro="citations">
296 <citation type="doi">DOI: 10.1002/humu.21517</citation>
297 <citation type="doi">DOI: 10.1002/humu.22376</citation>
298 <citation type="doi">DOI: 10.1002/humu.22932</citation>
299 <citation type="doi">doi: 10.1093/hmg/ddu733</citation>
300 <citation type="doi">doi: 10.1093/nar/gku1206</citation>
301 <citation type="doi">doi: 10.3389/fgene.2012.00035</citation>
302 </expand>
303 </tool>