Mercurial > repos > ryanmorin > nextgen_variant_identification
comparison SNV/annotate.xml @ 0:74f5ea818cea
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author | ryanmorin |
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date | Wed, 12 Oct 2011 19:50:38 -0400 |
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-1:000000000000 | 0:74f5ea818cea |
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1 <tool id="snv_annotate" name="SNV Annotator"> | |
2 <requirements> | |
3 <requirement type="package">SNVMix</requirement> | |
4 </requirements> | |
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> | |
6 <command interpreter="python"> | |
7 annotate.py | |
8 -i $input_codon | |
9 -o $output_anno | |
10 </command> | |
11 <inputs> | |
12 <param name="input_codon" type="data" format="tabular" label="Select the codon-linked file to annotate" /> | |
13 </inputs> | |
14 | |
15 <outputs> | |
16 <data format="tabular" name="output_anno" label="${tool.name}: annotated SNV calls" /> | |
17 </outputs> | |
18 <help> | |
19 | |
20 **What it does** | |
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). | |
22 Requires input produced by the "SNP filtering and pre-annotation" tool | |
23 | |
24 The additional columns are as follows: | |
25 1) Mutated form of the codon | |
26 2) Reference amino acid at that position | |
27 3) mutant amino acid at that position | |
28 4) CODING or SYNONYMOUS | |
29 5) Mutation with position and wild-type amino acid (separated by semicolon for genes with multiple transcripts) | |
30 | |
31 Example input: | |
32 chr7:148139660 ENSG00000106462 -1 TAC 2 602;646; ENST00000350995;ENST00000320356; T A T:39,A:25,0.0000000000,1.0000000000,0.0000000000,2 | |
33 | |
34 Example output: | |
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 | |
36 | |
37 </help> | |
38 </tool> |