Mercurial > repos > ryanmorin > nextgen_variant_identification
diff 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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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/SNV/annotate.xml Wed Oct 12 19:50:38 2011 -0400 @@ -0,0 +1,38 @@ +<tool id="snv_annotate" name="SNV Annotator"> + <requirements> + <requirement type="package">SNVMix</requirement> + </requirements> + <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> + <command interpreter="python"> + annotate.py + -i $input_codon + -o $output_anno + </command> + <inputs> + <param name="input_codon" type="data" format="tabular" label="Select the codon-linked file to annotate" /> +</inputs> + + <outputs> + <data format="tabular" name="output_anno" label="${tool.name}: annotated SNV calls" /> + </outputs> + <help> + +**What it does** +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). +Requires input produced by the "SNP filtering and pre-annotation" tool + +The additional columns are as follows: +1) Mutated form of the codon +2) Reference amino acid at that position +3) mutant amino acid at that position +4) CODING or SYNONYMOUS +5) Mutation with position and wild-type amino acid (separated by semicolon for genes with multiple transcripts) + +Example input: +chr7:148139660 ENSG00000106462 -1 TAC 2 602;646; ENST00000350995;ENST00000320356; T A T:39,A:25,0.0000000000,1.0000000000,0.0000000000,2 + +Example output: +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 + + </help> +</tool>