Mercurial > repos > iuc > snpsift_dbnsfp

annotate snpSift_dbnsfp.xml @ 277:6c1a0c6cf28c draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
author iuc
date Tue, 07 Jun 2016 09:41:50 -0400
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children 02f54bf45aaf
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277
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
iuc
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1 <tool id="snpSift_dbnsfp" name="SnpSift dbNSFP" version="@WRAPPER_VERSION@.0">
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
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2 <description>Add Annotations from dbNSFP or similar annotation DBs</description>
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
iuc
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3 <macros>
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
iuc
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4 <import>snpSift_macros.xml</import>
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
iuc
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5 </macros>
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
iuc
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6 <expand macro="requirements" />
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
iuc
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7 <expand macro="stdio" />
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
iuc
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8 <expand macro="version_command" />
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
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9 <command><![CDATA[
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
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10 java -Xmx6G -jar "\$SNPEFF_JAR_PATH/SnpSift.jar" dbnsfp -v
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
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11 #if $db.dbsrc == 'cached':
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
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12 -db "$db.dbnsfp"
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
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13 #if $db.annotations and str($db.annotations) != '':
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
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14 -f "$db.annotations"
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
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15 #end if
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
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16 #else:
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
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17 -db "${db.dbnsfpdb.extra_files_path}/${db.dbnsfpdb.metadata.bgzip}"
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
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18 #if $db.annotations and str($db.annotations) != '':
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
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19 -f "$db.annotations"
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
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20 #end if
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
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21 #end if
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
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22 "$input" > "$output"
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
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23 2> tmp.err && grep -v file tmp.err
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
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24 ]]>
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
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25 </command>
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
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26 <inputs>
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
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27 <param name="input" type="data" format="vcf" label="Variant input file in VCF format"/>
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
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28 <conditional name="db">
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
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29 <param name="dbsrc" type="select" label="dbNSFP ">
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
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30 <option value="cached">Locally installed dbNSFP database </option>
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
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31 <option value="history">dbNSFP database from your history</option>
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
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32 </param>
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
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33 <when value="cached">
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
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34 <param name="dbnsfp" type="select" label="Genome">
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
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35 <options from_data_table="snpsift_dbnsfps">
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
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36 <column name="name" index="2"/>
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
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37 <column name="value" index="3"/>
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
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38 </options>
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
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39 </param>
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
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40 <param name="annotations" type="select" multiple="true" display="checkboxes" label="Annotate with">
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
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41 <options from_data_table="snpsift_dbnsfps">
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
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42 <column name="name" index="4"/>
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
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43 <column name="value" index="4"/>
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
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44 <filter type="param_value" ref="dbnsfp" column="3" />
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
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45 <filter type="multiple_splitter" column="4" separator=","/>
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
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46 </options>
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
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47 </param>
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
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48 </when>
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
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49 <when value="history">
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
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50 <param name="dbnsfpdb" type="data" format="snpsiftdbnsfp" label="DbNSFP"/>
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
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51 <param name="annotations" type="select" multiple="true" display="checkboxes" label="Annotate with">
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
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52 <options>
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53 <filter type="data_meta" ref="dbnsfpdb" key="annotation" />
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54 </options>
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
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55 </param>
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
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56 </when>
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57 </conditional>
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58 </inputs>
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
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59 <outputs>
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
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60 <data format="vcf" name="output" />
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61 </outputs>
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
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62 <tests>
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63 <test>
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64 <param name="input" ftype="vcf" value="test_annotate_in.vcf.vcf"/>
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
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65 <param name="dbsrc" value="history"/>
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
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66 <param name="dbnsfpdb" value="test_dbnsfpdb.tabular" ftype="dbnsfp.tabular" />
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67 <annotations value="aaref,aaalt,genename,aapos,SIFT_score"/>
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
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68 <output name="output">
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69 <assert_contents>
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70 <has_text text="dbNSFP_SIFT_score=0.15" />
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71 </assert_contents>
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72 </output>
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
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73 </test>
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
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74 </tests>
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
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75 <help><![CDATA[
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76
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
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77 The dbNSFP is an integrated database of functional predictions from multiple algorithms (SIFT, Polyphen2, LRT and MutationTaster, PhyloP and GERP++, etc.).
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
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78 It contains variant annotations such as:
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
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79
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
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80
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
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81 1000Gp1_AC
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
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82 Alternative allele counts in the whole 1000 genomes phase 1 (1000Gp1) data
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
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83 1000Gp1_AF
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
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84 Alternative allele frequency in the whole 1000Gp1 data
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
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85 1000Gp1_AFR_AC
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
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86 Alternative allele counts in the 1000Gp1 African descendent samples
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
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87 1000Gp1_AFR_AF
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
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88 Alternative allele frequency in the 1000Gp1 African descendent samples
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
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89 1000Gp1_AMR_AC
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
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90 Alternative allele counts in the 1000Gp1 American descendent samples
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
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91 1000Gp1_AMR_AF
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
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92 Alternative allele frequency in the 1000Gp1 American descendent samples
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
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93 1000Gp1_ASN_AC
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
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94 Alternative allele counts in the 1000Gp1 Asian descendent samples
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
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95 1000Gp1_ASN_AF
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
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96 Alternative allele frequency in the 1000Gp1 Asian descendent samples
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
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97 1000Gp1_EUR_AC
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
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98 Alternative allele counts in the 1000Gp1 European descendent samples
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
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99 1000Gp1_EUR_AF
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
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100 Alternative allele frequency in the 1000Gp1 European descendent samples
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
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101 aaalt
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
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102 Alternative amino acid. "." if the variant is a splicing site SNP (2bp on each end of an intron)
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
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103 aapos
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
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104 Amino acid position as to the protein. "-1" if the variant is a splicing site SNP (2bp on each end of an intron)
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
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105 aapos_SIFT
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
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106 ENSP id and amino acid positions corresponding to SIFT scores. Multiple entries separated by ";"
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
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107 aapos_FATHMM
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
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108 ENSP id and amino acid positions corresponding to FATHMM scores. Multiple entries separated by ";"
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
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109 aaref
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
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110 Reference amino acid. "." if the variant is a splicing site SNP (2bp on each end of an intron)
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
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111 alt
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
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112 Alternative nucleotide allele (as on the + strand)
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
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113 Ancestral_allele
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
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114 Ancestral allele (based on 1000 genomes reference data)
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
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115 cds_strand
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
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116 Coding sequence (CDS) strand (+ or -)
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
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117 chr
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
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118 Chromosome number
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
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119 codonpos
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
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120 Position on the codon (1, 2 or 3)
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
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121 Ensembl_geneid
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
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122 Ensembl gene ID
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
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123 Ensembl_transcriptid
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
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124 Ensembl transcript IDs (separated by ";")
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
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125 ESP6500_AA_AF
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
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126 Alternative allele frequency in the African American samples of the NHLBI GO Exome Sequencing Project (ESP6500 data set)
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
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127 ESP6500_EA_AF
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
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128 Alternative allele frequency in the European American samples of the NHLBI GO Exome Sequencing Project (ESP6500 data set)
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
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129 FATHMM_pred
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
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130 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 ";"
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
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131 FATHMM_rankscore
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
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132 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
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
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133 FATHMM_score
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
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134 FATHMM default score (FATHMMori)
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
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135 fold-degenerate
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
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136 Degenerate type (0, 2 or 3)
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
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137 genename
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
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138 Gene name; if the non-synonymous SNP can be assigned to multiple genes, gene names are separated by ";"
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
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139 GERP++_NR
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
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140 GERP++ neutral rate
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
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141 GERP++_RS
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
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142 GERP++ RS score, the larger the score, the more conserved the site
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
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143 GERP++_RS_rankscore
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
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144 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
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
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145 hg18_pos(1-coor)
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
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146 Physical position on the chromosome as to hg18 (1-based coordinate)
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
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147 Interpro_domain
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
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148 Domain or conserved site on which the variant locates
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
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149 LR_pred
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
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150 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
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
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151 LR_rankscore
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
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152 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
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
iuc
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diff changeset
153 LR_score
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
iuc
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diff changeset
154 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
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
iuc
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diff changeset
155 LRT_Omega
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
iuc
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diff changeset
156 Estimated nonsynonymous-to-synonymous-rate ratio (Omega, reported by LRT)
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
iuc
parents:
diff changeset
157 LRT_converted_rankscore
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
iuc
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diff changeset
158 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
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
iuc
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diff changeset
159 LRT_pred
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
iuc
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diff changeset
160 LRT prediction, D(eleterious), N(eutral) or U(nknown), which is not solely determined by the score
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
iuc
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diff changeset
161 LRT_score
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
iuc
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diff changeset
162 The original LRT two-sided p-value (LRTori), ranges from 0 to 1
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
iuc
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diff changeset
163 MutationAssessor_pred
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
iuc
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diff changeset
164 MutationAssessor's functional impact of a variant
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
iuc
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diff changeset
165 MutationAssessor_rankscore
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
iuc
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diff changeset
166 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
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
iuc
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diff changeset
167 MutationAssessor_score
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
iuc
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diff changeset
168 MutationAssessor functional impact combined score (MAori)
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
iuc
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diff changeset
169 MutationTaster_converted_rankscore
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
iuc
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diff changeset
170 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
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
iuc
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diff changeset
171 MutationTaster_pred
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
iuc
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diff changeset
172 MutationTaster prediction
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
iuc
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diff changeset
173 MutationTaster_score
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
iuc
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diff changeset
174 MutationTaster p-value (MTori), ranges from 0 to 1
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
iuc
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diff changeset
175 phastCons46way_placental
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
iuc
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diff changeset
176 phastCons conservation score based on the multiple alignments of 33 placental mammal genomes (including human). The larger the score, the more conserved the site
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
iuc
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diff changeset
177 phastCons46way_placental_rankscore
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
iuc
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diff changeset
178 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
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
iuc
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diff changeset
179 phastCons46way_primate
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
iuc
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diff changeset
180 phastCons conservation score based on the multiple alignments of 10 primate genomes (including human). The larger the score, the more conserved the site
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
iuc
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diff changeset
181 phastCons46way_primate_rankscore
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
iuc
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diff changeset
182 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
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
iuc
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diff changeset
183 phastCons100way_vertebrate
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
iuc
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diff changeset
184 phastCons conservation score based on the multiple alignments of 100 vertebrate genomes (including human). The larger the score, the more conserved the site
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
iuc
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diff changeset
185 phastCons100way_vertebrate_rankscore
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
iuc
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diff changeset
186 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
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
iuc
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diff changeset
187 phyloP46way_placental
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
iuc
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diff changeset
188 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
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
iuc
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diff changeset
189 phyloP46way_placental_rankscore
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
iuc
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diff changeset
190 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
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
iuc
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diff changeset
191 phyloP46way_primate
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
iuc
parents:
diff changeset
192 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
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
iuc
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diff changeset
193 phyloP46way_primate_rankscore
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
iuc
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194 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
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
iuc
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diff changeset
195 phyloP100way_vertebrate
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
iuc
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diff changeset
196 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
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
iuc
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diff changeset
197 phyloP100way_vertebrate_rankscore
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
iuc
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diff changeset
198 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
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
iuc
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diff changeset
199 Polyphen2_HDIV_pred
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
iuc
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200 Polyphen2 prediction based on HumDiv
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
iuc
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diff changeset
201 Polyphen2_HDIV_rankscore
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
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diff changeset
202 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
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
iuc
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diff changeset
203 Polyphen2_HDIV_score
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
iuc
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diff changeset
204 Polyphen2 score based on HumDiv, i.e. hdiv_prob. The score ranges from 0 to 1. Multiple entries separated by ";"
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
iuc
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diff changeset
205 Polyphen2_HVAR_pred
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
iuc
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diff changeset
206 Polyphen2 prediction based on HumVar
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
iuc
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diff changeset
207 Polyphen2_HVAR_rankscore
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
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208 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
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
iuc
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diff changeset
209 Polyphen2_HVAR_score
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
iuc
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diff changeset
210 Polyphen2 score based on HumVar, i.e. hvar_prob. The score ranges from 0 to 1. Multiple entries separated by ";"
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
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211 pos(1-coor)
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
iuc
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212 Physical position on the chromosome as to hg19 (1-based coordinate)
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
iuc
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diff changeset
213 RadialSVM_pred
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
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diff changeset
214 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
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
iuc
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diff changeset
215 RadialSVM_rankscore
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
iuc
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diff changeset
216 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
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
iuc
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diff changeset
217 RadialSVM_score
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
iuc
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218 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
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
iuc
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219 ref
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
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220 Reference nucleotide allele (as on the + strand)
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221 refcodon
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222 Reference codon
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223 Reliability_index
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224 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
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225 SIFT_converted_rankscore
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226 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
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227 SIFT_pred
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228 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 ";"
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229 SIFT_score
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230 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 ";"
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231 SiPhy_29way_logOdds
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232 SiPhy score based on 29 mammals genomes. The larger the score, the more conserved the site
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233 SiPhy_29way_pi
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234 The estimated stationary distribution of A, C, G and T at the site, using SiPhy algorithm based on 29 mammals genomes
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235 SLR_test_statistic
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236 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
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237 Uniprot_aapos
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238 Amino acid position as to Uniprot. Multiple entries separated by ";"
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239 Uniprot_acc
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240 Uniprot accession number. Multiple entries separated by ";"
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241 Uniprot_id
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242 Uniprot ID number. Multiple entries separated by ";"
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243 UniSNP_ids
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244 rs numbers from UniSNP, which is a cleaned version of dbSNP build 129, in format: rs number1;rs number2;...
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245
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246
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247 The website for dbNSFP database is https://sites.google.com/site/jpopgen/dbNSFP and there is only annotation for human genome builds.
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248
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249 The procedure for preparing the dbNSFP data for use in SnpSift dbnsfp is in the SnpSift documentation:
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250 *( It also provides links for dbNSFP databases prebuilt for SnpSift )*
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251 http://snpeff.sourceforge.net/SnpSift.html#dbNSFP
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252
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253 However, any dbNSFP-like tabular file that be can used with SnpSift dbnsfp if it has::
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254
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255 - The first line of the file must be column headers that name the annotations.
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256 - The first 4 columns are required and must be::
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257 1. chromosome
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258 2. position in chromosome
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259 3. reference base
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260 4. alternate base
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261
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262 For example:
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263
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264 ::
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265
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266 #chr pos(1-coor) ref alt aaref aaalt genename SIFT_score
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267 1 69134 A C E A OR4F5 0.03
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268 1 69134 A G E G OR4F5 0.09
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269 1 69134 A T E V OR4F5 0.03
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270 4 100239319 T A H L ADH1B 0
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271 4 100239319 T C H R ADH1B 0.15
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272 4 100239319 T G H P ADH1B 0
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273
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274
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275 The galaxy datatypes for dbNSFP can automatically convert the specially formatted tabular file for use by SnpSift dbNSFP:
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276 1. Upload the tabular file, set the datatype as: **"dbnsfp.tabular"**
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277 2. Edit the history dataset attributes (pencil icon): Use "Convert Format" to convert the **"dbnsfp.tabular"** to the correct format for SnpSift dbnsfp: **"snpsiftdbnsfp"**.
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278
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279
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280 @EXTERNAL_DOCUMENTATION@
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281 http://snpeff.sourceforge.net/SnpSift.html#dbNSFP
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282
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283 @CITATION_SECTION@
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284
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285 ]]>
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286 </help>
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287 <expand macro="citations">
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288 <citation type="doi">DOI: 10.1002/humu.21517</citation>
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289 <citation type="doi">DOI: 10.1002/humu.22376</citation>
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290 <citation type="doi">DOI: 10.1002/humu.22932</citation>
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291 <citation type="doi">doi: 10.1093/hmg/ddu733</citation>
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292 <citation type="doi">doi: 10.1093/nar/gku1206</citation>
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293 <citation type="doi">doi: 10.3389/fgene.2012.00035</citation>
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294 </expand>
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295 </tool>