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1 <tool id="snv_annotate" name="SNV Annotator">
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2 <requirements>
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3 <requirement type="package">SNVMix</requirement>
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4 </requirements>
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5 <description>Annotates filtered SNVMix output that has been attached to codon information (outputs the same data with additional columns describing the predicted effect of the SNV)</description>
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6 <command interpreter="python">
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7 annotate.py
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8 -i $input_codon
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9 -o $output_anno
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10 </command>
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11 <inputs>
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12 <param name="input_codon" type="data" format="tabular" label="Select the codon-linked file to annotate" />
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13 </inputs>
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14
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15 <outputs>
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16 <data format="tabular" name="output_anno" label="${tool.name}: annotated SNV calls" />
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17 </outputs>
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18 <help>
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19
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20 **What it does**
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21 Annotates filtered SNVMix output that has been attached to codon information (outputs the same data with additional columns describing the predicted effect of the SNV).
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22 Requires input produced by the "SNP filtering and pre-annotation" tool
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23
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24 The additional columns are as follows:
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25 1) Mutated form of the codon
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26 2) Reference amino acid at that position
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27 3) mutant amino acid at that position
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28 4) CODING or SYNONYMOUS
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29 5) Mutation with position and wild-type amino acid (separated by semicolon for genes with multiple transcripts)
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30
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31 Example input:
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32 chr7:148139660 ENSG00000106462 -1 TAC 2 602;646; ENST00000350995;ENST00000320356; T A T:39,A:25,0.0000000000,1.0000000000,0.0000000000,2
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33
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34 Example output:
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35 chr7:148139660 ENSG00000106462 -1 TAC 2 602;646; ENST00000350995;ENST00000320356; T A T:39,A:25,0.0000000000,1.0000000000,0.0000000000,2 TTC Y F CODING Y602F;Y646F
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36
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37 </help>
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38 </tool>
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