VEP: add Paralogues plugin (e114)

root/documentation/vep.conf

@@ -243,6 +243,12 @@
         description=Provides scores from Multiplexed Assays of Variant Effect for variants as reported by <a target="_blank" href="https://www.mavedb.org">MaveDB</a> database. (<a target="_blank" href="https://raw.githubusercontent.com/ensembl-variation/VEP_plugins/main/MaveDB.pm">plugin details</a>)
         default=0
       </MaveDB>
+      <Paralogues>
+        type=String
+        description=Retrieves ClinVar variants that overlap genomic coordinates corresponding to aligned amino acid positions in paralogous proteins. The following options are available:<table class="table"><thead><tr><th>Argument</th><th>Description</th><th>Default</th></tr></thead><tbody><tr><td><code>clinsig</code></td><td>Clinical significance term to filter variants; use <code>clnsig=ignore</code> to fetch all paralogue variants, regardless of clinical significance</td><td><code>clnsig<wbr>=<wbr>pathogenic</code></td></tr><tr><td><code>clnsig_match</code></td><td> Type of match when filtering variants based on clinical significance: <code>partial</code>, <code>exact</code> or <code>regex</code></td><td><code>clnsig_match<wbr>=<wbr>partial</code></td></tr><tr><td><code>fields</code></td><td>Colon-separated list of information from paralogue variants to output; use <code>fields=all</code> to print all fields</td><td><code>fields<wbr>=<wbr>identifier<wbr>:<wbr>alleles<wbr>:<wbr>clinical_significance</code></td></tr><tr><td><code>min_perc_cov</code></td><td>Minimum alignment percentage of the peptide associated with the input variant</td><td><code>min_perc_cov=0</code></td></tr><tr><td><code>min_perc_pos</code></td><td>Minimum percentage of positivity (similarity) between both homologues</td><td><code>min_perc_pos=50</code></td></tr></tbody></table>(<a target="_blank" href="https://raw.githubusercontent.com/ensembl-variation/VEP_plugins/main/Paralogues.pm">plugin details</a>)
+        default=Not used
+        example=clnsig=<wbr>pathogenic,<wbr>clnsig_match=<wbr>exact,<wbr>fields=<wbr>all
+      </Paralogues>
       <NMD>
         type=Boolean
         description=Predicts if a variant allows the transcript escape nonsense-mediated mRNA decay. (<a target="_blank" href="https://raw.githubusercontent.com/ensembl-variation/VEP_plugins/main/NMD.pm">plugin details</a>)
@@ -592,6 +598,12 @@
         description=Provides scores from Multiplexed Assays of Variant Effect for variants as reported by <a target="_blank" href="https://www.mavedb.org">MaveDB</a> database. (<a target="_blank" href="https://raw.githubusercontent.com/ensembl-variation/VEP_plugins/main/MaveDB.pm">plugin details</a>)
         default=0
       </MaveDB>
+      <Paralogues>
+        type=String
+        description=Retrieves ClinVar variants that overlap genomic coordinates corresponding to aligned amino acid positions in paralogous proteins. The following options are available:<table class="table"><thead><tr><th>Argument</th><th>Description</th><th>Default</th></tr></thead><tbody><tr><td><code>clinsig</code></td><td>Clinical significance term to filter variants; use <code>clnsig=ignore</code> to fetch all paralogue variants, regardless of clinical significance</td><td><code>clnsig<wbr>=<wbr>pathogenic</code></td></tr><tr><td><code>clnsig_match</code></td><td> Type of match when filtering variants based on clinical significance: <code>partial</code>, <code>exact</code> or <code>regex</code></td><td><code>clnsig_match<wbr>=<wbr>partial</code></td></tr><tr><td><code>fields</code></td><td>Colon-separated list of information from paralogue variants to output; use <code>fields=all</code> to print all fields</td><td><code>fields<wbr>=<wbr>identifier<wbr>:<wbr>alleles<wbr>:<wbr>clinical_significance</code></td></tr><tr><td><code>min_perc_cov</code></td><td>Minimum alignment percentage of the peptide associated with the input variant</td><td><code>min_perc_cov=0</code></td></tr><tr><td><code>min_perc_pos</code></td><td>Minimum percentage of positivity (similarity) between both homologues</td><td><code>min_perc_pos=50</code></td></tr></tbody></table>(<a target="_blank" href="https://raw.githubusercontent.com/ensembl-variation/VEP_plugins/main/Paralogues.pm">plugin details</a>)
+        default=Not used
+        example=clnsig=<wbr>pathogenic,<wbr>clnsig_match=<wbr>exact,<wbr>fields=<wbr>all
+      </Paralogues>
       <NMD>
         type=Boolean
         description=Predicts if a variant allows the transcript escape nonsense-mediated mRNA decay. (<a target="_blank" href="https://raw.githubusercontent.com/ensembl-variation/VEP_plugins/main/NMD.pm">plugin details</a>)
@@ -929,6 +941,12 @@
         description=Provides scores from Multiplexed Assays of Variant Effect for variants as reported by <a target="_blank" href="https://www.mavedb.org">MaveDB</a> database. (<a target="_blank" href="https://raw.githubusercontent.com/ensembl-variation/VEP_plugins/main/MaveDB.pm">plugin details</a>)
         default=0
       </MaveDB>
+      <Paralogues>
+        type=String
+        description=Retrieves ClinVar variants that overlap genomic coordinates corresponding to aligned amino acid positions in paralogous proteins. The following options are available:<table class="table"><thead><tr><th>Argument</th><th>Description</th><th>Default</th></tr></thead><tbody><tr><td><code>clinsig</code></td><td>Clinical significance term to filter variants; use <code>clnsig=ignore</code> to fetch all paralogue variants, regardless of clinical significance</td><td><code>clnsig<wbr>=<wbr>pathogenic</code></td></tr><tr><td><code>clnsig_match</code></td><td> Type of match when filtering variants based on clinical significance: <code>partial</code>, <code>exact</code> or <code>regex</code></td><td><code>clnsig_match<wbr>=<wbr>partial</code></td></tr><tr><td><code>fields</code></td><td>Colon-separated list of information from paralogue variants to output; use <code>fields=all</code> to print all fields</td><td><code>fields<wbr>=<wbr>identifier<wbr>:<wbr>alleles<wbr>:<wbr>clinical_significance</code></td></tr><tr><td><code>min_perc_cov</code></td><td>Minimum alignment percentage of the peptide associated with the input variant</td><td><code>min_perc_cov=0</code></td></tr><tr><td><code>min_perc_pos</code></td><td>Minimum percentage of positivity (similarity) between both homologues</td><td><code>min_perc_pos=50</code></td></tr></tbody></table>(<a target="_blank" href="https://raw.githubusercontent.com/ensembl-variation/VEP_plugins/main/Paralogues.pm">plugin details</a>)
+        default=Not used
+        example=clnsig=<wbr>pathogenic,<wbr>clnsig_match=<wbr>exact,<wbr>fields=<wbr>all
+      </Paralogues>
       <NMD>
         type=Boolean
         description=Predicts if a variant allows the transcript escape nonsense-mediated mRNA decay. (<a target="_blank" href="https://raw.githubusercontent.com/ensembl-variation/VEP_plugins/main/NMD.pm">plugin details</a>)
@@ -1260,6 +1278,12 @@
         description=Provides scores from Multiplexed Assays of Variant Effect for variants as reported by <a target="_blank" href="https://www.mavedb.org">MaveDB</a> database. (<a target="_blank" href="https://raw.githubusercontent.com/ensembl-variation/VEP_plugins/main/MaveDB.pm">plugin details</a>)
         default=0
       </MaveDB>
+      <Paralogues>
+        type=String
+        description=Retrieves ClinVar variants that overlap genomic coordinates corresponding to aligned amino acid positions in paralogous proteins. The following options are available:<table class="table"><thead><tr><th>Argument</th><th>Description</th><th>Default</th></tr></thead><tbody><tr><td><code>clinsig</code></td><td>Clinical significance term to filter variants; use <code>clnsig=ignore</code> to fetch all paralogue variants, regardless of clinical significance</td><td><code>clnsig<wbr>=<wbr>pathogenic</code></td></tr><tr><td><code>clnsig_match</code></td><td> Type of match when filtering variants based on clinical significance: <code>partial</code>, <code>exact</code> or <code>regex</code></td><td><code>clnsig_match<wbr>=<wbr>partial</code></td></tr><tr><td><code>fields</code></td><td>Colon-separated list of information from paralogue variants to output; use <code>fields=all</code> to print all fields</td><td><code>fields<wbr>=<wbr>identifier<wbr>:<wbr>alleles<wbr>:<wbr>clinical_significance</code></td></tr><tr><td><code>min_perc_cov</code></td><td>Minimum alignment percentage of the peptide associated with the input variant</td><td><code>min_perc_cov=0</code></td></tr><tr><td><code>min_perc_pos</code></td><td>Minimum percentage of positivity (similarity) between both homologues</td><td><code>min_perc_pos=50</code></td></tr></tbody></table>(<a target="_blank" href="https://raw.githubusercontent.com/ensembl-variation/VEP_plugins/main/Paralogues.pm">plugin details</a>)
+        default=Not used
+        example=clnsig=<wbr>pathogenic,<wbr>clnsig_match=<wbr>exact,<wbr>fields=<wbr>all
+      </Paralogues>
       <NMD>
         type=Boolean
         description=Predicts if a variant allows the transcript escape nonsense-mediated mRNA decay. (<a target="_blank" href="https://raw.githubusercontent.com/ensembl-variation/VEP_plugins/main/NMD.pm">plugin details</a>)
@@ -1602,6 +1626,12 @@
         description=Provides scores from Multiplexed Assays of Variant Effect for variants as reported by <a target="_blank" href="https://www.mavedb.org">MaveDB</a> database. (<a target="_blank" href="https://raw.githubusercontent.com/ensembl-variation/VEP_plugins/main/MaveDB.pm">plugin details</a>)
         default=0
       </MaveDB>
+      <Paralogues>
+        type=String
+        description=Retrieves ClinVar variants that overlap genomic coordinates corresponding to aligned amino acid positions in paralogous proteins. The following options are available:<table class="table"><thead><tr><th>Argument</th><th>Description</th><th>Default</th></tr></thead><tbody><tr><td><code>clinsig</code></td><td>Clinical significance term to filter variants; use <code>clnsig=ignore</code> to fetch all paralogue variants, regardless of clinical significance</td><td><code>clnsig<wbr>=<wbr>pathogenic</code></td></tr><tr><td><code>clnsig_match</code></td><td> Type of match when filtering variants based on clinical significance: <code>partial</code>, <code>exact</code> or <code>regex</code></td><td><code>clnsig_match<wbr>=<wbr>partial</code></td></tr><tr><td><code>fields</code></td><td>Colon-separated list of information from paralogue variants to output; use <code>fields=all</code> to print all fields</td><td><code>fields<wbr>=<wbr>identifier<wbr>:<wbr>alleles<wbr>:<wbr>clinical_significance</code></td></tr><tr><td><code>min_perc_cov</code></td><td>Minimum alignment percentage of the peptide associated with the input variant</td><td><code>min_perc_cov=0</code></td></tr><tr><td><code>min_perc_pos</code></td><td>Minimum percentage of positivity (similarity) between both homologues</td><td><code>min_perc_pos=50</code></td></tr></tbody></table>(<a target="_blank" href="https://raw.githubusercontent.com/ensembl-variation/VEP_plugins/main/Paralogues.pm">plugin details</a>)
+        default=Not used
+        example=clnsig=<wbr>pathogenic,<wbr>clnsig_match=<wbr>exact,<wbr>fields=<wbr>all
+      </Paralogues>
       <NMD>
         type=Boolean
         description=Predicts if a variant allows the transcript escape nonsense-mediated mRNA decay. (<a target="_blank" href="https://raw.githubusercontent.com/ensembl-variation/VEP_plugins/main/NMD.pm">plugin details</a>)
@@ -1952,6 +1982,12 @@
         description=Provides scores from Multiplexed Assays of Variant Effect for variants as reported by <a target="_blank" href="https://www.mavedb.org">MaveDB</a> database. (<a target="_blank" href="https://raw.githubusercontent.com/ensembl-variation/VEP_plugins/main/MaveDB.pm">plugin details</a>)
         default=0
       </MaveDB>
+      <Paralogues>
+        type=String
+        description=Retrieves ClinVar variants that overlap genomic coordinates corresponding to aligned amino acid positions in paralogous proteins. The following options are available:<table class="table"><thead><tr><th>Argument</th><th>Description</th><th>Default</th></tr></thead><tbody><tr><td><code>clinsig</code></td><td>Clinical significance term to filter variants; use <code>clnsig=ignore</code> to fetch all paralogue variants, regardless of clinical significance</td><td><code>clnsig<wbr>=<wbr>pathogenic</code></td></tr><tr><td><code>clnsig_match</code></td><td> Type of match when filtering variants based on clinical significance: <code>partial</code>, <code>exact</code> or <code>regex</code></td><td><code>clnsig_match<wbr>=<wbr>partial</code></td></tr><tr><td><code>fields</code></td><td>Colon-separated list of information from paralogue variants to output; use <code>fields=all</code> to print all fields</td><td><code>fields<wbr>=<wbr>identifier<wbr>:<wbr>alleles<wbr>:<wbr>clinical_significance</code></td></tr><tr><td><code>min_perc_cov</code></td><td>Minimum alignment percentage of the peptide associated with the input variant</td><td><code>min_perc_cov=0</code></td></tr><tr><td><code>min_perc_pos</code></td><td>Minimum percentage of positivity (similarity) between both homologues</td><td><code>min_perc_pos=50</code></td></tr></tbody></table>(<a target="_blank" href="https://raw.githubusercontent.com/ensembl-variation/VEP_plugins/main/Paralogues.pm">plugin details</a>)
+        default=Not used
+        example=clnsig=<wbr>pathogenic,<wbr>clnsig_match=<wbr>exact,<wbr>fields=<wbr>all
+      </Paralogues>
       <NMD>
         type=Boolean
         description=Predicts if a variant allows the transcript escape nonsense-mediated mRNA decay. (<a target="_blank" href="https://raw.githubusercontent.com/ensembl-variation/VEP_plugins/main/NMD.pm">plugin details</a>)