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Commit ec33d641 authored by Syed Hossain's avatar Syed Hossain Committed by Natalie Willhoft
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Deprecate Mastermind plugin

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Branches release/114
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lib/EnsEMBL/REST/Model/ga4gh/Beacon.pm
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− 1
View file @ ec33d641
......@@ -765,7 +765,6 @@ sub configure_vep {
# VEP plugins to run
my $plugins_to_use = {
'IntAct' => 'all=1',
'Mastermind' => '0,0,1',
'GO' => '1',
'Phenotypes' => '1',
'CADD' => '1',
......
root/documentation/vep.conf
+ 0
− 30
View file @ ec33d641
......@@ -300,11 +300,6 @@
description=Retrieves overlapping phenotype information (<a target="_blank" href="https://raw.githubusercontent.com/ensembl-variation/VEP_plugins/main/Phenotypes.pm">plugin details</a>)
default=0
</Phenotypes>
<Mastermind>
type=Boolean
description= Variants that have clinical evidence cited in the medical literature reported by <a target="_blank" href="https://www.genomenon.com/mastermind">Mastermind Genomic Search Engine</a> (<a target="_blank" href="https://raw.githubusercontent.com/ensembl-variation/VEP_plugins/main/Mastermind.pm">plugin details</a>)
default=0
</Mastermind>
<CADD>
type=Boolean
description=Include CADD (Combined Annotation Dependent Depletion) deleteriousness scores for single nucleotide variants (also supports sus_scrofa), indels and structural variants (only supported in GRCh38). Following options can be given: <b>snv</b>, <b>indels</b>, <b>snv_indels</b>, and <b>sv</b>. Providing 1 is also supported which is same as providing <b>snv_indels</b>. Caution to be taken while using snv, indels or snv_indels options with structural variants as input. It can match unnecessary huge amount of lines in annotation file and in such cases no CADD annotation will be made. See <a target="_blank" href="https://cadd.gs.washington.edu/">license</a>. (<a target="_blank" href="https://raw.githubusercontent.com/ensembl-variation/VEP_plugins/main/CADD.pm">plugin details</a>)
......@@ -665,11 +660,6 @@
description=Retrieves overlapping phenotype information (<a target="_blank" href="https://raw.githubusercontent.com/ensembl-variation/VEP_plugins/main/Phenotypes.pm">plugin details</a>)
default=0
</Phenotypes>
<Mastermind>
type=Boolean
description= Variants that have clinical evidence cited in the medical literature reported by <a target="_blank" href="https://www.genomenon.com/mastermind">Mastermind Genomic Search Engine</a> (<a target="_blank" href="https://raw.githubusercontent.com/ensembl-variation/VEP_plugins/main/Mastermind.pm">plugin details</a>)
default=0
</Mastermind>
<CADD>
type=Boolean
description=Include CADD (Combined Annotation Dependent Depletion) deleteriousness scores for single nucleotide variants (also supports sus_scrofa), indels and structural variants (only supported in GRCh38). Following options can be given: <b>snv</b>, <b>indels</b>, <b>snv_indels</b>, and <b>sv</b>. Providing 1 is also supported which is same as providing <b>snv_indels</b>. Caution to be taken while using snv, indels or snv_indels options with structural variants as input. It can match unnecessary huge amount of lines in annotation file and in such cases no CADD annotation will be made. See <a target="_blank" href="https://cadd.gs.washington.edu/">license</a>. (<a target="_blank" href="https://raw.githubusercontent.com/ensembl-variation/VEP_plugins/main/CADD.pm">plugin details</a>)
......@@ -1018,11 +1008,6 @@
description=Retrieves overlapping phenotype information (<a target="_blank" href="https://raw.githubusercontent.com/ensembl-variation/VEP_plugins/main/Phenotypes.pm">plugin details</a>)
default=0
</Phenotypes>
<Mastermind>
type=Boolean
description= Variants that have clinical evidence cited in the medical literature reported by <a target="_blank" href="https://www.genomenon.com/mastermind">Mastermind Genomic Search Engine</a> (<a target="_blank" href="https://raw.githubusercontent.com/ensembl-variation/VEP_plugins/main/Mastermind.pm">plugin details</a>)
default=0
</Mastermind>
<CADD>
type=Boolean
description=Include CADD (Combined Annotation Dependent Depletion) deleteriousness scores for single nucleotide variants (also supports sus_scrofa), indels and structural variants (only supported in GRCh38). Following options can be given: <b>snv</b>, <b>indels</b>, <b>snv_indels</b>, and <b>sv</b>. Providing 1 is also supported which is same as providing <b>snv_indels</b>. Caution to be taken while using snv, indels or snv_indels options with structural variants as input. It can match unnecessary huge amount of lines in annotation file and in such cases no CADD annotation will be made. See <a target="_blank" href="https://cadd.gs.washington.edu/">license</a>. (<a target="_blank" href="https://raw.githubusercontent.com/ensembl-variation/VEP_plugins/main/CADD.pm">plugin details</a>)
......@@ -1365,11 +1350,6 @@
description=Retrieves overlapping phenotype information (<a target="_blank" href="https://raw.githubusercontent.com/ensembl-variation/VEP_plugins/main/Phenotypes.pm">plugin details</a>)
default=0
</Phenotypes>
<Mastermind>
type=Boolean
description= Variants that have clinical evidence cited in the medical literature reported by <a target="_blank" href="https://www.genomenon.com/mastermind">Mastermind Genomic Search Engine</a> (<a target="_blank" href="https://raw.githubusercontent.com/ensembl-variation/VEP_plugins/main/Mastermind.pm">plugin details</a>)
default=0
</Mastermind>
<CADD>
type=Boolean
description=Include CADD (Combined Annotation Dependent Depletion) deleteriousness scores for single nucleotide variants (also supports sus_scrofa), indels and structural variants (only supported in GRCh38). Following options can be given: <b>snv</b>, <b>indels</b>, <b>snv_indels</b>, and <b>sv</b>. Providing 1 is also supported which is same as providing <b>snv_indels</b>. Caution to be taken while using snv, indels or snv_indels options with structural variants as input. It can match unnecessary huge amount of lines in annotation file and in such cases no CADD annotation will be made. See <a target="_blank" href="https://cadd.gs.washington.edu/">license</a>. (<a target="_blank" href="https://raw.githubusercontent.com/ensembl-variation/VEP_plugins/main/CADD.pm">plugin details</a>)
......@@ -1723,11 +1703,6 @@
description=Retrieves overlapping phenotype information (<a target="_blank" href="https://raw.githubusercontent.com/ensembl-variation/VEP_plugins/main/Phenotypes.pm">plugin details</a>)
default=0
</Phenotypes>
<Mastermind>
type=Boolean
description= Variants that have clinical evidence cited in the medical literature reported by <a target="_blank" href="https://www.genomenon.com/mastermind">Mastermind Genomic Search Engine</a> (<a target="_blank" href="https://raw.githubusercontent.com/ensembl-variation/VEP_plugins/main/Mastermind.pm">plugin details</a>)
default=0
</Mastermind>
<CADD>
type=Boolean
description=Include CADD (Combined Annotation Dependent Depletion) deleteriousness scores for single nucleotide variants (also supports sus_scrofa), indels and structural variants (only supported in GRCh38). Following options can be given: <b>snv</b>, <b>indels</b>, <b>snv_indels</b>, and <b>sv</b>. Providing 1 is also supported which is same as providing <b>snv_indels</b>. Caution to be taken while using snv, indels or snv_indels options with structural variants as input. It can match unnecessary huge amount of lines in annotation file and in such cases no CADD annotation will be made. See <a target="_blank" href="https://cadd.gs.washington.edu/">license</a>. (<a target="_blank" href="https://raw.githubusercontent.com/ensembl-variation/VEP_plugins/main/CADD.pm">plugin details</a>)
......@@ -2089,11 +2064,6 @@
description=Retrieves overlapping phenotype information (<a target="_blank" href="https://raw.githubusercontent.com/ensembl-variation/VEP_plugins/main/Phenotypes.pm">plugin details</a>)
default=0
</Phenotypes>
<Mastermind>
type=Boolean
description= Variants that have clinical evidence cited in the medical literature reported by <a target="_blank" href="https://www.genomenon.com/mastermind">Mastermind Genomic Search Engine</a> (<a target="_blank" href="https://raw.githubusercontent.com/ensembl-variation/VEP_plugins/main/Mastermind.pm">plugin details</a>)
default=0
</Mastermind>
<CADD>
type=Boolean
description=Include CADD (Combined Annotation Dependent Depletion) deleteriousness scores for single nucleotide variants (also supports sus_scrofa), indels and structural variants (only supported in GRCh38). Following options can be given: <b>snv</b>, <b>indels</b>, <b>snv_indels</b>, and <b>sv</b>. Providing 1 is also supported which is same as providing <b>snv_indels</b>. Caution to be taken while using snv, indels or snv_indels options with structural variants as input. It can match unnecessary huge amount of lines in annotation file and in such cases no CADD annotation will be made. See <a target="_blank" href="https://cadd.gs.washington.edu/">license</a>. (<a target="_blank" href="https://raw.githubusercontent.com/ensembl-variation/VEP_plugins/main/CADD.pm">plugin details</a>)
......
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