Mercurial > repos > iuc > snpsift_dbnsfp

annotate snpSift_dbnsfp.xml @ 271:4da149ea747e draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 97a064489364118d108b0dd2cfb4d9bc53080837
author iuc
date Thu, 19 Nov 2015 14:52:30 -0500
parents f6fbf582d8f4
children 9d6fbd3a6e9b
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f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
iuc
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1 <tool id="snpSift_dbnsfp" name="SnpSift dbNSFP" version="4.0.0">
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
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2 <description>Add Annotations from dbNSFP</description>
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
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3 <macros>
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
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4 <import>snpSift_macros.xml</import>
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
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5 </macros>
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
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6 <expand macro="requirements" />
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
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7 <expand macro="stdio" />
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
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8 <command>
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
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9 java -Xmx6G -jar \$SNPEFF_JAR_PATH/SnpSift.jar dbnsfp -v
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
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10 #if $db.dbsrc == 'cached' :
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
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11 -db $db.dbnsfp
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
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12 #if $db.annotations and $db.annotations.__str__ != '':
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
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13 -f "$db.annotations"
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
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14 #end if
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
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15 #else :
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
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16 -db "${db.dbnsfpdb.extra_files_path}/${db.dbnsfpdb.metadata.bgzip}"
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
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17 #if $db.annotations and $db.annotations.__str__ != '':
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
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18 -f "$db.annotations"
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
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19 #end if
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
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20 #end if
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
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21 $input > $output
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
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22 2> tmp.err &amp;&amp; grep -v file tmp.err
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
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23 </command>
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
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24 <inputs>
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
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25 <param name="input" type="data" format="vcf" label="Variant input file in VCF format"/>
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
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26 <conditional name="db">
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
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27 <param name="dbsrc" type="select" label="dbNSFP ">
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
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28 <option value="cached">Locally installed dbNSFP database </option>
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
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29 <option value="history">dbNSFP database from your history</option>
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
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30 </param>
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
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31 <when value="cached">
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
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32 <param name="dbnsfp" type="select" label="Genome">
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
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33 <options from_data_table="snpsift_dbnsfp">
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
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34 <column name="name" index="1"/>
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
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35 <column name="value" index="2"/>
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
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36 </options>
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
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37 </param>
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
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38 <param name="annotations" type="select" multiple="true" display="checkboxes" label="Annotate with">
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
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39 <options from_data_table="snpsift_dbnsfp">
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
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40 <column name="name" index="3"/>
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
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41 <column name="value" index="3"/>
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
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42 <filter type="param_value" ref="dbnsfp" column="2" />
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
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43 <filter type="multiple_splitter" column="3" separator=","/>
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
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44 </options>
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
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45 </param>
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
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46 </when>
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
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47 <when value="history">
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
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48 <param name="dbnsfpdb" type="data" format="snpsiftdbnsfp" label="DbNSFP"/>
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
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49 <param name="annotations" type="select" multiple="true" display="checkboxes" label="Annotate with">
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
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50 <options>
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
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51 <filter type="data_meta" ref="dbnsfpdb" key="annotation" />
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52 </options>
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
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53 </param>
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
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54 </when>
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55 </conditional>
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
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56 </inputs>
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
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57 <outputs>
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
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58 <data format="vcf" name="output" />
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59 </outputs>
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
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60 <tests>
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61 <test>
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62 <param name="input" ftype="vcf" value="test_annotate_in.vcf.vcf"/>
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63 <param name="dbsrc" value="history"/>
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64 <param name="dbnsfpdb" value="test_dbnsfpdb.tabular" ftype="dbnsfp.tabular" />
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65 <annotations value="aaref,aaalt,genename,aapos,SIFT_score"/>
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
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66 <output name="output">
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67 <assert_contents>
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68 <has_text text="dbNSFP_SIFT_score=0.15" />
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69 </assert_contents>
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
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70 </output>
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71 </test>
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72 </tests>
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73 <help>
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74
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
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75 The dbNSFP is an integrated database of functional predictions from multiple algorithms (SIFT, Polyphen2, LRT and MutationTaster, PhyloP and GERP++, etc.).
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
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76
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
iuc
parents:
diff changeset
77
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
iuc
parents:
diff changeset
78 1000Gp1_AC
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
iuc
parents:
diff changeset
79 Alternative allele counts in the whole 1000 genomes phase 1 (1000Gp1) data
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
iuc
parents:
diff changeset
80 1000Gp1_AF
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
iuc
parents:
diff changeset
81 Alternative allele frequency in the whole 1000Gp1 data
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
iuc
parents:
diff changeset
82 1000Gp1_AFR_AC
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
iuc
parents:
diff changeset
83 Alternative allele counts in the 1000Gp1 African descendent samples
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
iuc
parents:
diff changeset
84 1000Gp1_AFR_AF
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
iuc
parents:
diff changeset
85 Alternative allele frequency in the 1000Gp1 African descendent samples
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
iuc
parents:
diff changeset
86 1000Gp1_AMR_AC
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
iuc
parents:
diff changeset
87 Alternative allele counts in the 1000Gp1 American descendent samples
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
iuc
parents:
diff changeset
88 1000Gp1_AMR_AF
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
iuc
parents:
diff changeset
89 Alternative allele frequency in the 1000Gp1 American descendent samples
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
iuc
parents:
diff changeset
90 1000Gp1_ASN_AC
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
iuc
parents:
diff changeset
91 Alternative allele counts in the 1000Gp1 Asian descendent samples
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
iuc
parents:
diff changeset
92 1000Gp1_ASN_AF
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
iuc
parents:
diff changeset
93 Alternative allele frequency in the 1000Gp1 Asian descendent samples
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
iuc
parents:
diff changeset
94 1000Gp1_EUR_AC
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
iuc
parents:
diff changeset
95 Alternative allele counts in the 1000Gp1 European descendent samples
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
iuc
parents:
diff changeset
96 1000Gp1_EUR_AF
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
iuc
parents:
diff changeset
97 Alternative allele frequency in the 1000Gp1 European descendent samples
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
iuc
parents:
diff changeset
98 aaalt
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
iuc
parents:
diff changeset
99 Alternative amino acid. "." if the variant is a splicing site SNP (2bp on each end of an intron)
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
iuc
parents:
diff changeset
100 aapos
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
iuc
parents:
diff changeset
101 Amino acid position as to the protein. "-1" if the variant is a splicing site SNP (2bp on each end of an intron)
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
iuc
parents:
diff changeset
102 aapos_SIFT
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
iuc
parents:
diff changeset
103 ENSP id and amino acid positions corresponding to SIFT scores. Multiple entries separated by ";"
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
iuc
parents:
diff changeset
104 aapos_FATHMM
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
iuc
parents:
diff changeset
105 ENSP id and amino acid positions corresponding to FATHMM scores. Multiple entries separated by ";"
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
iuc
parents:
diff changeset
106 aaref
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
iuc
parents:
diff changeset
107 Reference amino acid. "." if the variant is a splicing site SNP (2bp on each end of an intron)
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
iuc
parents:
diff changeset
108 alt
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
iuc
parents:
diff changeset
109 Alternative nucleotide allele (as on the + strand)
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
iuc
parents:
diff changeset
110 Ancestral_allele
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
iuc
parents:
diff changeset
111 Ancestral allele (based on 1000 genomes reference data)
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
iuc
parents:
diff changeset
112 cds_strand
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
iuc
parents:
diff changeset
113 Coding sequence (CDS) strand (+ or -)
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
iuc
parents:
diff changeset
114 chr
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
iuc
parents:
diff changeset
115 Chromosome number
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
iuc
parents:
diff changeset
116 codonpos
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
iuc
parents:
diff changeset
117 Position on the codon (1, 2 or 3)
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
iuc
parents:
diff changeset
118 Ensembl_geneid
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
iuc
parents:
diff changeset
119 Ensembl gene ID
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
iuc
parents:
diff changeset
120 Ensembl_transcriptid
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
iuc
parents:
diff changeset
121 Ensembl transcript IDs (separated by ";")
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
iuc
parents:
diff changeset
122 ESP6500_AA_AF
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
iuc
parents:
diff changeset
123 Alternative allele frequency in the African American samples of the NHLBI GO Exome Sequencing Project (ESP6500 data set)
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
iuc
parents:
diff changeset
124 ESP6500_EA_AF
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
iuc
parents:
diff changeset
125 Alternative allele frequency in the European American samples of the NHLBI GO Exome Sequencing Project (ESP6500 data set)
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
iuc
parents:
diff changeset
126 FATHMM_pred
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
iuc
parents:
diff changeset
127 If a FATHMM_score is &lt;=-1.5 (or rankscore &lt;=0.81415) the corresponding non-synonymous SNP is predicted as "D(AMAGING)"; otherwise it is predicted as "T(OLERATED)". Multiple predictions separated by ";"
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
iuc
parents:
diff changeset
128 FATHMM_rankscore
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
iuc
parents:
diff changeset
129 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
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
iuc
parents:
diff changeset
130 FATHMM_score
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
iuc
parents:
diff changeset
131 FATHMM default score (FATHMMori)
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
iuc
parents:
diff changeset
132 fold-degenerate
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
iuc
parents:
diff changeset
133 Degenerate type (0, 2 or 3)
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
iuc
parents:
diff changeset
134 genename
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
iuc
parents:
diff changeset
135 Gene name; if the non-synonymous SNP can be assigned to multiple genes, gene names are separated by ";"
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
iuc
parents:
diff changeset
136 GERP++_NR
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
iuc
parents:
diff changeset
137 GERP++ neutral rate
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
iuc
parents:
diff changeset
138 GERP++_RS
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
iuc
parents:
diff changeset
139 GERP++ RS score, the larger the score, the more conserved the site
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
iuc
parents:
diff changeset
140 GERP++_RS_rankscore
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
iuc
parents:
diff changeset
141 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
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
iuc
parents:
diff changeset
142 hg18_pos(1-coor)
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
iuc
parents:
diff changeset
143 Physical position on the chromosome as to hg18 (1-based coordinate)
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
iuc
parents:
diff changeset
144 Interpro_domain
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
iuc
parents:
diff changeset
145 Domain or conserved site on which the variant locates
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
iuc
parents:
diff changeset
146 LR_pred
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
iuc
parents:
diff changeset
147 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
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
iuc
parents:
diff changeset
148 LR_rankscore
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
iuc
parents:
diff changeset
149 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
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
iuc
parents:
diff changeset
150 LR_score
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
iuc
parents:
diff changeset
151 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
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
iuc
parents:
diff changeset
152 LRT_Omega
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
iuc
parents:
diff changeset
153 Estimated nonsynonymous-to-synonymous-rate ratio (Omega, reported by LRT)
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
iuc
parents:
diff changeset
154 LRT_converted_rankscore
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
iuc
parents:
diff changeset
155 LRTori scores were first converted as LRTnew=1-LRTori*0.5 if Omega&lt;1, or LRTnew=LRTori*0.5 if Omega&gt;=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
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
iuc
parents:
diff changeset
156 LRT_pred
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
iuc
parents:
diff changeset
157 LRT prediction, D(eleterious), N(eutral) or U(nknown), which is not solely determined by the score
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
iuc
parents:
diff changeset
158 LRT_score
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
iuc
parents:
diff changeset
159 The original LRT two-sided p-value (LRTori), ranges from 0 to 1
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
iuc
parents:
diff changeset
160 MutationAssessor_pred
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
iuc
parents:
diff changeset
161 MutationAssessor's functional impact of a variant
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
iuc
parents:
diff changeset
162 MutationAssessor_rankscore
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
iuc
parents:
diff changeset
163 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
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
iuc
parents:
diff changeset
164 MutationAssessor_score
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
iuc
parents:
diff changeset
165 MutationAssessor functional impact combined score (MAori)
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
iuc
parents:
diff changeset
166 MutationTaster_converted_rankscore
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
iuc
parents:
diff changeset
167 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
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
iuc
parents:
diff changeset
168 MutationTaster_pred
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
iuc
parents:
diff changeset
169 MutationTaster prediction
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
iuc
parents:
diff changeset
170 MutationTaster_score
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
iuc
parents:
diff changeset
171 MutationTaster p-value (MTori), ranges from 0 to 1
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
iuc
parents:
diff changeset
172 phastCons46way_placental
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
iuc
parents:
diff changeset
173 phastCons conservation score based on the multiple alignments of 33 placental mammal genomes (including human). The larger the score, the more conserved the site
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
iuc
parents:
diff changeset
174 phastCons46way_placental_rankscore
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
iuc
parents:
diff changeset
175 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
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
iuc
parents:
diff changeset
176 phastCons46way_primate
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
iuc
parents:
diff changeset
177 phastCons conservation score based on the multiple alignments of 10 primate genomes (including human). The larger the score, the more conserved the site
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
iuc
parents:
diff changeset
178 phastCons46way_primate_rankscore
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
iuc
parents:
diff changeset
179 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
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
iuc
parents:
diff changeset
180 phastCons100way_vertebrate
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
iuc
parents:
diff changeset
181 phastCons conservation score based on the multiple alignments of 100 vertebrate genomes (including human). The larger the score, the more conserved the site
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
iuc
parents:
diff changeset
182 phastCons100way_vertebrate_rankscore
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
iuc
parents:
diff changeset
183 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
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
iuc
parents:
diff changeset
184 phyloP46way_placental
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
iuc
parents:
diff changeset
185 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
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
iuc
parents:
diff changeset
186 phyloP46way_placental_rankscore
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
iuc
parents:
diff changeset
187 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
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
iuc
parents:
diff changeset
188 phyloP46way_primate
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
iuc
parents:
diff changeset
189 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
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
iuc
parents:
diff changeset
190 phyloP46way_primate_rankscore
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
iuc
parents:
diff changeset
191 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
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
iuc
parents:
diff changeset
192 phyloP100way_vertebrate
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
iuc
parents:
diff changeset
193 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
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
iuc
parents:
diff changeset
194 phyloP100way_vertebrate_rankscore
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
iuc
parents:
diff changeset
195 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
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
iuc
parents:
diff changeset
196 Polyphen2_HDIV_pred
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
iuc
parents:
diff changeset
197 Polyphen2 prediction based on HumDiv
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
iuc
parents:
diff changeset
198 Polyphen2_HDIV_rankscore
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
iuc
parents:
diff changeset
199 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
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
iuc
parents:
diff changeset
200 Polyphen2_HDIV_score
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
iuc
parents:
diff changeset
201 Polyphen2 score based on HumDiv, i.e. hdiv_prob. The score ranges from 0 to 1. Multiple entries separated by ";"
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
iuc
parents:
diff changeset
202 Polyphen2_HVAR_pred
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
iuc
parents:
diff changeset
203 Polyphen2 prediction based on HumVar
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
iuc
parents:
diff changeset
204 Polyphen2_HVAR_rankscore
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
iuc
parents:
diff changeset
205 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
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
iuc
parents:
diff changeset
206 Polyphen2_HVAR_score
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
iuc
parents:
diff changeset
207 Polyphen2 score based on HumVar, i.e. hvar_prob. The score ranges from 0 to 1. Multiple entries separated by ";"
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
iuc
parents:
diff changeset
208 pos(1-coor)
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
iuc
parents:
diff changeset
209 Physical position on the chromosome as to hg19 (1-based coordinate)
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
iuc
parents:
diff changeset
210 RadialSVM_pred
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
iuc
parents:
diff changeset
211 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
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
iuc
parents:
diff changeset
212 RadialSVM_rankscore
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
iuc
parents:
diff changeset
213 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
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
iuc
parents:
diff changeset
214 RadialSVM_score
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
iuc
parents:
diff changeset
215 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
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
iuc
parents:
diff changeset
216 ref
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
iuc
parents:
diff changeset
217 Reference nucleotide allele (as on the + strand)
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
iuc
parents:
diff changeset
218 refcodon
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
iuc
parents:
diff changeset
219 Reference codon
f6fbf582d8f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
iuc
parents:
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220 Reliability_index
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221 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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222 SIFT_converted_rankscore
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223 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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224 SIFT_pred
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225 If SIFTori is smaller than 0.05 (rankscore&gt;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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226 SIFT_score
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227 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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228 SiPhy_29way_logOdds
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229 SiPhy score based on 29 mammals genomes. The larger the score, the more conserved the site
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230 SiPhy_29way_pi
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231 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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232 SLR_test_statistic
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233 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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234 Uniprot_aapos
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235 Amino acid position as to Uniprot. Multiple entries separated by ";"
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236 Uniprot_acc
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237 Uniprot accession number. Multiple entries separated by ";"
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238 Uniprot_id
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239 Uniprot ID number. Multiple entries separated by ";"
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240 UniSNP_ids
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241 rs numbers from UniSNP, which is a cleaned version of dbSNP build 129, in format: rs number1;rs number2;...
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242
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243
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244 The website for dbNSFP database is https://sites.google.com/site/jpopgen/dbNSFP and there is only annotation for human hg18 and hg19 genome builds.
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245
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246 However, any dbNSFP-like tabular file that be can used with SnpSift dbnsfp if it has::
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247
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248 - The first line of the file must be column headers that name the annotations.
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249 - The first 4 columns are required and must be::
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250 1. chromosome
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251 2. position in chromosome
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252 3. reference base
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253 4. alternate base
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254
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255 For example:
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256
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257 ::
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258
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259 #chr pos(1-coor) ref alt aaref aaalt genename SIFT_score
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260 1 69134 A C E A OR4F5 0.03
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261 1 69134 A G E G OR4F5 0.09
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262 1 69134 A T E V OR4F5 0.03
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263 4 100239319 T A H L ADH1B 0
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264 4 100239319 T C H R ADH1B 0.15
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265 4 100239319 T G H P ADH1B 0
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266
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267
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268 The uploaded tabular file should be set to datatype: "dbnsfp.tabular"
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269 Using "Convert Format" the "dbnsfp.tabular" can be converted to the correct format for SnpSift dbnsfp.
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270
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271 The procedure for preparing the dbNSFP data for use in SnpSift dbnsfp is in the SnpSift documentation.
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272
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273
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274 @EXTERNAL_DOCUMENTATION@
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275 http://snpeff.sourceforge.net/SnpSift.html#dbNSFP
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276
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277 @CITATION_SECTION@
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278
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279
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280 </help>
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281 </tool>