Mercurial > repos > elixir-it > vinyl

comparison VINYL_M.xml @ 1:da94ac699bfa draft default tip

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author elixir-it
date Wed, 15 Jul 2020 07:52:10 +0000
parents 5d1070767d27
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0:5d1070767d27 1:da94ac699bfa
101 </outputs> 101 </outputs>
102 <stdio> 102 <stdio>
103 </stdio> 103 </stdio>
104 <tests> 104 <tests>
105 <test> 105 <test>
106 <param name="VcfFile" value="RIS.vcf" ftype="vcf" /> 106 <param name="VcfFile" value="TSI_annotated.vcf" ftype="vcf" />
107 <output name="ofile" file="VINYL_output1_test" ftype="tabular" /> 107 <param name="lgenes" value="DCM_genes.tabular" ftype="tabular" />
108 <param name="qfile" value="qfile.txt" ftype="txt" />
109 <param name="kfile" value="kfile.txt" ftype="txt" />
110 <param name="efile" value="efile.txt" ftype="txt" />
111 <output name="ofile" file="VINYL_output1_test.tabular" ftype="tabular" />
108 <output name="ovcfile" file="VINYL_output2_test.vcf" ftype="vcf" /> 112 <output name="ovcfile" file="VINYL_output2_test.vcf" ftype="vcf" />
109 <output name="osummary" file="VINYL_output3_test" ftype="tabular" /> 113 <output name="osummary" file="VINYL_output3_test.tabular" ftype="tabular" />
114 <output name="log" file="log.txt" ftype="txt" />
110 </test> 115 </test>
111 </tests> 116 </tests>
112 <help> 117 <help>
113 **What it does** 118 **What it does**
114 VINYL is a software designed to assist in variant prioritization in medium-large cohort of patients. The program computes an aggregate score, which is based on an extensive collection of publicly available annoations, in order to identify/prioritize variants that are likely to be pathogenic or have a clinical significance. In order to derive an optimal cut off score for the variants, VINYL uses a strategy based on "survival analysis", where the pathogenicity score distribution of the affected individuals is compared with a matched cohort of unaffected individuals. 119 VINYL is a software designed to assist in variant prioritization in medium-large cohort of patients. The program computes an aggregate score, which is based on an extensive collection of publicly available annoations, in order to identify/prioritize variants that are likely to be pathogenic or have a clinical significance. In order to derive an optimal cut off score for the variants, VINYL uses a strategy based on "survival analysis", where the pathogenicity score distribution of the affected individuals is compared with a matched cohort of unaffected individuals.