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comparison tools/annovar/annovar.xml @ 2:565c0e690238 draft

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Added support for LJB2, COSMIC67, CLINVAR and NCI60. Fixed dgv annotation to use new UCSC table dgvMerged instead.
author saskia-hiltemann
date Mon, 18 Nov 2013 10:32:33 -0500
parents 7d9353127f8a
children ff5325029a8e
comparison
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1:7d9353127f8a 2:565c0e690238
5 <requirement type="package" version="1.7">cgatools</requirement> 5 <requirement type="package" version="1.7">cgatools</requirement>
6 </requirements> 6 </requirements>
7 7
8 <command interpreter="bash"> 8 <command interpreter="bash">
9 annovar.sh 9 annovar.sh
10 --impactscores ${impactscores}
11 --esp ${esp} 10 --esp ${esp}
12 --gerp ${gerp} 11 --gerp ${gerp}
13 --cosmic61 ${cosmic61} 12 --cosmic61 ${cosmic61}
14 --cosmic63 ${cosmic63} 13 --cosmic63 ${cosmic63}
15 --cosmic64 ${cosmic64} 14 --cosmic64 ${cosmic64}
16 --cosmic65 ${cosmic65} 15 --cosmic65 ${cosmic65}
16 --cosmic67 ${cosmic67}
17 --outall ${annotated} 17 --outall ${annotated}
18 --outinvalid ${invalid} 18 --outinvalid ${invalid}
19 --dorunannovar ${dorun} 19 --dorunannovar ${dorun}
20 --inputfile ${infile} 20 --inputfile ${infile}
21 --buildver ${reference.fields.dbkey} 21 --buildver ${reference.fields.dbkey}
55 --VCF N 55 --VCF N
56 #end if 56 #end if
57 --cg46 ${cgfortysix} 57 --cg46 ${cgfortysix}
58 --cg69 ${cgsixtynine} 58 --cg69 ${cgsixtynine}
59 --ver1000g ${ver1000g} 59 --ver1000g ${ver1000g}
60 --hgvs ${hgvs}
61 --otherinfo ${otherinfo}
62 --newimpactscores ${newimpactscores}
63 --clinvar ${clinvar}
60 64
61 </command> 65 </command>
62 66
63 <inputs> 67 <inputs>
64 <param name="dorun" type="hidden" value="Y"/> <!-- will add tool in future to filter on annovar columns, then will call annovar.sh with dorun==N --> 68 <param name="dorun" type="hidden" value="Y"/> <!-- will add tool in future to filter on annovar columns, then will call annovar.sh with dorun==N -->
96 <param name="geneanno" type="select" label="Select Gene Annotation(s)" multiple="true" optional="true" display="checkboxes"> 100 <param name="geneanno" type="select" label="Select Gene Annotation(s)" multiple="true" optional="true" display="checkboxes">
97 <option value="refSeq" selected="true" > RefSeq </option> 101 <option value="refSeq" selected="true" > RefSeq </option>
98 <option value="knowngene"> UCSC KnownGene </option> 102 <option value="knowngene"> UCSC KnownGene </option>
99 <option value="ensgene" > Ensembl </option> 103 <option value="ensgene" > Ensembl </option>
100 </param> 104 </param>
101 105 <param name="hgvs" type="boolean" checked="False" truevalue="-hgvs" falsevalue="N" label="Use HGVS nomenclature for RefSeq annotation" help="if checked, cDNA level annotation is compatible with HGVS"/>
106
102 107
103 <!-- region-based annotation --> 108 <!-- region-based annotation -->
104 <param name="cytoband" type="boolean" checked="False" truevalue="Y" falsevalue="N" label="Cytogenic band Annotation?" help="This option identifies Giemsa-stained chromosomes bands, (e.g. 1q21.1-q23.3)."/> 109 <param name="cytoband" type="boolean" checked="False" truevalue="Y" falsevalue="N" label="Cytogenic band Annotation?" help="This option identifies Giemsa-stained chromosomes bands, (e.g. 1q21.1-q23.3)."/>
105 <param name="tfbs" type="boolean" checked="False" truevalue="Y" falsevalue="N" label="Transcription Factor Binding Site Annotation?"/> 110 <param name="tfbs" type="boolean" checked="False" truevalue="Y" falsevalue="N" label="Transcription Factor Binding Site Annotation?"/>
106 <param name="mce" type="boolean" checked="False" truevalue="Y" falsevalue="N" label="Most Conserved Elements Annotation?" help="This option phastCons 44-way alignments to annotate variants that fall within conserved genomic regions."/> 111 <param name="mce" type="boolean" checked="False" truevalue="Y" falsevalue="N" label="Most Conserved Elements Annotation?" help="This option phastCons 44-way alignments to annotate variants that fall within conserved genomic regions."/>
152 </param> 157 </param>
153 158
154 159
155 <param name="gerp" type="boolean" checked="False" truevalue="Y" falsevalue="N" label="GERP++ Annotation?" help="GERP identifies constrained elements in multiple alignments by quantifying substitution deficits (see http://mendel.stanford.edu/SidowLab/downloads/gerp/ for details) This option annotates those variants having GERP++>2 in human genome, as this threshold is typically regarded as evolutionarily conserved and potentially functional"/> 160 <param name="gerp" type="boolean" checked="False" truevalue="Y" falsevalue="N" label="GERP++ Annotation?" help="GERP identifies constrained elements in multiple alignments by quantifying substitution deficits (see http://mendel.stanford.edu/SidowLab/downloads/gerp/ for details) This option annotates those variants having GERP++>2 in human genome, as this threshold is typically regarded as evolutionarily conserved and potentially functional"/>
156 161
162 <param name="clinvar" type="boolean" checked="False" truevalue="Y" falsevalue="N" label="CLINVAR Annotation? (hg19 only)" help="version 2013-11-05. Annotations include Variant Clinical Significance (unknown, untested, non-pathogenic, probable-non-pathogenic, probable-pathogenic, pathogenic, drug-response, histocompatibility, other) and Variant disease name."/>
163 <param name="nci60" type="boolean" checked="False" truevalue="Y" falsevalue="N" label="Annotate with NCI60? (hg19 only)" help="NCI-60 exome allele frequency data"/>
157 <param name="cgfortysix" type="boolean" checked="False" truevalue="Y" falsevalue="N" label="Complete Genomics 46 Genomes?" help="Diversity Panel; 46 unrelated individuals"/> 164 <param name="cgfortysix" type="boolean" checked="False" truevalue="Y" falsevalue="N" label="Complete Genomics 46 Genomes?" help="Diversity Panel; 46 unrelated individuals"/>
158 <param name="cgsixtynine" type="boolean" checked="False" truevalue="Y" falsevalue="N" label="Complete Genomics 69 Genomes?" help="Diversity Panel, Pedigree, YRI trio and PUR trio"/> 165 <param name="cgsixtynine" type="boolean" checked="False" truevalue="Y" falsevalue="N" label="Complete Genomics 69 Genomes?" help="Diversity Panel, Pedigree, YRI trio and PUR trio"/>
159 <param name="cosmic61" type="boolean" checked="False" truevalue="Y" falsevalue="N" label="Annotate with COSMIC61? (hg19 only)"/> 166 <param name="cosmic61" type="boolean" checked="False" truevalue="Y" falsevalue="N" label="Annotate with COSMIC61? (hg19 only)"/>
160 <param name="cosmic63" type="boolean" checked="False" truevalue="Y" falsevalue="N" label="Annotate with COSMIC63? (hg19 only)"/> 167 <param name="cosmic63" type="boolean" checked="False" truevalue="Y" falsevalue="N" label="Annotate with COSMIC63? (hg19 only)"/>
161 <param name="cosmic64" type="boolean" checked="False" truevalue="Y" falsevalue="N" label="Annotate with COSMIC64? (hg19 only)"/> 168 <param name="cosmic64" type="boolean" checked="False" truevalue="Y" falsevalue="N" label="Annotate with COSMIC64? (hg19 only)"/>
162 <param name="cosmic65" type="boolean" checked="False" truevalue="Y" falsevalue="N" label="Annotate with COSMIC65? (hg19 only)"/> 169 <param name="cosmic65" type="boolean" checked="False" truevalue="Y" falsevalue="N" label="Annotate with COSMIC65? (hg19 only)"/>
163 170 <param name="cosmic67" type="boolean" checked="False" truevalue="Y" falsevalue="N" label="Annotate with COSMIC67? (hg19 only)"/>
164 <param name="impactscores" type="select" label="Select functional impact scores annotate with" multiple="true" display="checkboxes" optional="true" help="LJB refers to Liu, Jian, Boerwinkle paper in Human Mutation, pubmed ID 21520341."> 171
172 <param name="newimpactscores" type="select" label="Select functional impact scores (LJB2)" multiple="true" display="checkboxes" optional="true" help="LJB refers to Liu, Jian, Boerwinkle paper in Human Mutation, pubmed ID 21520341. ">
173 <option value="ljb2_sift"> SIFT score </option>
174 <option value="ljb2_pp2hdiv"> PolyPhen2 HDIV score </option>
175 <option value="ljb2_pp2hvar" > PolyPhen2 HVAR score </option>
176 <option value="ljb2_mt" > MutationTaster score </option>
177 <option value="ljb2_ma" > MutationAssessor score </option>
178 <option value="ljb2_lrt"> LRT score (Likelihood Ratio Test) </option>
179 <option value="ljb2_phylop"> PhyloP score </option>
180 <option value="ljb2_fathmm" > FATHMM score </option>
181 <option value="ljb2_gerp"> GERP++ score </option>
182 <option value="ljb2_siphy"> SiPhy score </option>
183 </param>
184 <param name="otherinfo" type="boolean" checked="False" truevalue="-otherinfo" falsevalue="N" label="Also get predictions where possible?" help="e.g. annotated as -score,damaging- or -score,benign- instead of just score"/>
185
186 <!-- OBSOLETE impact scores, uncomment for backwards compatibility, add argument impactscores to command
187 <param name="impactscores" type="select" label="Select functional impact scores annotate with (OBSOLETE)" multiple="true" display="checkboxes" optional="true" help="LJB refers to Liu, Jian, Boerwinkle paper in Human Mutation, pubmed ID 21520341.">
165 <option value="avsift"> AV SIFT </option> 188 <option value="avsift"> AV SIFT </option>
166 <option value="ljbsift"> LJB SIFT (corresponds to 1-SIFT)</option> 189 <option value="ljbsift"> LJB SIFT (corresponds to 1-SIFT)</option>
167 <option value="pp2"> PolyPhen2 </option> 190 <option value="pp2"> PolyPhen2 </option>
168 <option value="mutationtaster" > MutationTaster </option> 191 <option value="mutationtaster" > MutationTaster </option>
169 <option value="lrt"> LRT (Likelihood Ratio Test) </option> 192 <option value="lrt"> LRT (Likelihood Ratio Test) </option>
170 <option value="phylop"> PhyloP </option> 193 <option value="phylop"> PhyloP </option>
171 </param> 194 </param>
172 195 -->
173 196
174 <!-- prefix for output file so you dont have to manually rename history items --> 197 <!-- prefix for output file so you dont have to manually rename history items -->
175 <param name="fname" type="text" value="" label="Prefix for your output file" help="Optional"/> 198 <param name="fname" type="text" value="" label="Prefix for your output file" help="Optional"/>
176 199
177 </inputs> 200 </inputs>
194 217
195 **Input Formats** 218 **Input Formats**
196 219
197 Input Formats may be one of the following: 220 Input Formats may be one of the following:
198 221
199 VCF file 222 VCF file
200 223 Complete Genomics varfile
201 Complete Genomics varfile 224
202 225 Custom tab-delimited file (specify chromosome, start, end, reference allele, observed allele columns)
203 Custom tab-delimited file (specify chromosome, start, end, reference allele, observed allele columns) 226
204 227 Custom tab-delimited CG-derived file (specify chromosome, start, end, reference allele, observed allele, varType columns)
205 Custom tab-delimited CG-derived file (specify chromosome, start, end, reference allele, observed allele, varType columns) 228
229
230 **Database Notes**
231
232 see ANNOVAR website for extensive documentation, a few notes on some of the databases:
233
234 **LJB2 Database**
235
236 PolyPhen2 HVAR should be used for diagnostics of Mendelian diseases, which requires distinguishing mutations with drastic effects from all the remaining human variation, including abundant mildly deleterious alleles.The authors recommend calling probably damaging if the score is between 0.909 and 1, and possibly damaging if the score is between 0.447 and 0.908, and benign if the score is between 0 and 0.446.
237
238 PolyPhen HDIV should be used when evaluating rare alleles at loci potentially involved in complex phenotypes, dense mapping of regions identified by genome-wide association studies, and analysis of natural selection from sequence data. The authors recommend calling probably damaging if the score is between 0.957 and 1, and possibly damaging if the score is between 0.453 and 0.956, and benign is the score is between 0 and 0.452.
206 239
207 </help> 240 </help>
208 241
209 </tool> 242 </tool>
210 243