Mercurial > repos > saskia-hiltemann > annovar
diff tools/annovar/annovar.xml @ 3:ff5325029a8e draft
Uploaded
author | saskia-hiltemann |
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date | Thu, 10 Apr 2014 09:15:32 -0400 |
parents | 565c0e690238 |
children | 4600be69b96f |
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--- a/tools/annovar/annovar.xml Mon Nov 18 10:32:33 2013 -0500 +++ b/tools/annovar/annovar.xml Thu Apr 10 09:15:32 2014 -0400 @@ -1,4 +1,4 @@ -<tool id="Annovar" name="ANNOVAR" version="2013aug"> +<tool id="AnnovarShed" name="ANNOVAR" version="2013aug"> <description> Annotate a file using ANNOVAR </description> <requirements> @@ -13,7 +13,8 @@ --cosmic63 ${cosmic63} --cosmic64 ${cosmic64} --cosmic65 ${cosmic65} - --cosmic67 ${cosmic67} + --cosmic67 ${cosmic67} + --cosmic68 ${cosmic68} --outall ${annotated} --outinvalid ${invalid} --dorunannovar ${dorun} @@ -130,7 +131,9 @@ <option value="snp135" > 135 (hg19 only) </option> <option value="snp135NonFlagged"> 135 NonFlagged </option> <option value="snp137" > 137 (hg19 only) </option> - <option value="snp137NonFlagged"> 137 NonFlagged </option> + <option value="snp137NonFlagged"> 137 NonFlagged </option> + <option value="snp138" > 138 (hg19 only) </option> + <option value="snp138NonFlagged"> 138 NonFlagged </option> </param> <param name="ver1000g" type="select" label="Select 1000Genomes Annotation(s)" multiple="true" display="checkboxes" optional="true" help="2012april database for ALL populations was converted to hg18 using the UCSC liftover program"> @@ -159,7 +162,7 @@ <param name="gerp" type="boolean" checked="False" truevalue="Y" falsevalue="N" label="GERP++ Annotation?" help="GERP identifies constrained elements in multiple alignments by quantifying substitution deficits (see http://mendel.stanford.edu/SidowLab/downloads/gerp/ for details) This option annotates those variants having GERP++>2 in human genome, as this threshold is typically regarded as evolutionarily conserved and potentially functional"/> - <param name="clinvar" type="boolean" checked="False" truevalue="Y" falsevalue="N" label="CLINVAR Annotation? (hg19 only)" help="version 2013-11-05. Annotations include Variant Clinical Significance (unknown, untested, non-pathogenic, probable-non-pathogenic, probable-pathogenic, pathogenic, drug-response, histocompatibility, other) and Variant disease name."/> + <param name="clinvar" type="boolean" checked="False" truevalue="Y" falsevalue="N" label="CLINVAR Annotation? (hg19 only)" help="version 2014-02-11. Annotations include Variant Clinical Significance (unknown, untested, non-pathogenic, probable-non-pathogenic, probable-pathogenic, pathogenic, drug-response, histocompatibility, other) and Variant disease name."/> <param name="nci60" type="boolean" checked="False" truevalue="Y" falsevalue="N" label="Annotate with NCI60? (hg19 only)" help="NCI-60 exome allele frequency data"/> <param name="cgfortysix" type="boolean" checked="False" truevalue="Y" falsevalue="N" label="Complete Genomics 46 Genomes?" help="Diversity Panel; 46 unrelated individuals"/> <param name="cgsixtynine" type="boolean" checked="False" truevalue="Y" falsevalue="N" label="Complete Genomics 69 Genomes?" help="Diversity Panel, Pedigree, YRI trio and PUR trio"/> @@ -168,6 +171,8 @@ <param name="cosmic64" type="boolean" checked="False" truevalue="Y" falsevalue="N" label="Annotate with COSMIC64? (hg19 only)"/> <param name="cosmic65" type="boolean" checked="False" truevalue="Y" falsevalue="N" label="Annotate with COSMIC65? (hg19 only)"/> <param name="cosmic67" type="boolean" checked="False" truevalue="Y" falsevalue="N" label="Annotate with COSMIC67? (hg19 only)"/> + <param name="cosmic68" type="boolean" checked="False" truevalue="Y" falsevalue="N" label="Annotate with COSMIC68? (hg19 only)"/> + <param name="newimpactscores" type="select" label="Select functional impact scores (LJB2)" multiple="true" display="checkboxes" optional="true" help="LJB refers to Liu, Jian, Boerwinkle paper in Human Mutation, pubmed ID 21520341. "> <option value="ljb2_sift"> SIFT score </option>