Mercurial > repos > elixir-it > vinyl_optimizer

comparison optimizer_genetic.xml @ 1:35c308dd6420 draft

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author elixir-it
date Wed, 22 Jul 2020 19:08:23 +0000
parents 4c6529d120c3
children 6e4eb4856874
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0:4c6529d120c3 1:35c308dd6420
147 </outputs> 147 </outputs>
148 <stdio> 148 <stdio>
149 </stdio> 149 </stdio>
150 <tests> 150 <tests>
151 <test> 151 <test>
152 <param name="fileR" value="R.csv" ftype="csv" /> 152 <param name="fileR" value="TSI_annotated.vcf" ftype="vcf" />
153 <param name="fileC" value="T.csv" ftype="csv" /> 153 <param name="fileC" value="sorrentino_annotated.vcf" ftype="vcf" />
154 <!-- default values--> 154 <param name="lgenes" value="DCM_genes.tabular" ftype="tabular" />
155 <param name="score_DB_MIN" value="1" type="float" min="1" max="20" /> 155 <param name="qfile" value="qfile.txt" ftype="txt" />
156 <param name="score_DB_MAX" value="20" type="float" min="1" max="20" /> 156 <param name="kfile" value="kfile.txt" ftype="txt" />
157 <param name="score_RV_MIN" value="1" type="float" min="1" max="20" /> 157 <param name="efile" value="efile.txt" ftype="txt" />
158 <param name="score_RV_MAX" value="20" type="float" min="1" max="20" /> 158 <param name="sfile" value="sfile.txt" ftype="txt" />
159 <param name="score_FE_MIN" value="1" min="1" max="20" type="float" /> 159 <output name="ofile" file="output_optimizer.tsv" ftype="tsv" />
160 <param name="score_FE_MAX" value="20" min="1" max="20" type="float" /> 160 <output name="log" file="log.txt" ftype="txt" />
161 <param name="score_NS_MIN" value="1" min="1" max="20" type="float" />
162 <param name="score_NS_MAX" value="20" min="1" max="20" type="float" />
163 <param name="score_OR_MIN" value="1" type="float" min="1" max="20" />
164 <param name="score_OR_MAX" value="20" type="float" min="1" max="20" />
165 <param name="score_eQ_MIN" value="1" min="1" max="20" type="float" />
166 <param name="score_eQ_MAX" value="20" min="1" max="20" type="float" />
167 <param name="score_AD_MIN" value="1" min="1" max="20" type="float" />
168 <param name="score_AD_MAX" value="20" min="1" max="20" type="float" />
169 <param name="score_T_MIN" value="1" min="1" max="20" type="float" />
170 <param name="score_T_MAX" value="20" min="1" max="20" type="float" />
171 <param name="score_GW_MIN" value="1" min="1" max="20" type="float" />
172 <param name="score_GW_MAX" value="20" min="1" max="20" type="float" />
173 <param name="score_M_MIN" value="1" min="1" max="20" type="float" />
174 <param name="score_M_MAX" value="20" min="1" max="20" type="float" />
175 <param name="score_R_MIN" value="1" min="1" max="10" type="float" />
176 <param name="score_R_MAX" value="20" min="1" max="20" type="float" />
177 <param name="score_SP_MIN" value="1" min="1" max="10" type="float" />
178 <param name="score_SP_MAX" value="20" min="1" max="20" type="float" />
179 <param name="nind" value="5" type="integer" />
180 <param name="AF" value="0.0001" min="0" max="1" type="float" />
181 <param name="AD" type="text" value="T" />
182 <param name="XL" type="text" value="F" />
183 <output name="ofile" file="optimizer_output_test.tsv" ftype="tsv" />
184 </test> 161 </test>
185 </tests> 162 </tests>
186 <help> 163 <help>
187 **What it does** 164 **What it does**
188 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 annotations, 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. 165 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 annotations, 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.