From f8fdf2056fb357a2e46637d5287029f2d3887595 Mon Sep 17 00:00:00 2001
From: Syed Nakib Hossain <snhossain@ebi.ac.uk>
Date: Mon, 16 Dec 2024 16:54:59 +0000
Subject: [PATCH] Deprecate Mastermind plugin
---
lib/EnsEMBL/REST/Model/ga4gh/Beacon.pm | 1 -
root/documentation/vep.conf | 30 --------------------------
2 files changed, 31 deletions(-)
diff --git a/lib/EnsEMBL/REST/Model/ga4gh/Beacon.pm b/lib/EnsEMBL/REST/Model/ga4gh/Beacon.pm
index 8ac8b918..75cc0d29 100644
--- a/lib/EnsEMBL/REST/Model/ga4gh/Beacon.pm
+++ b/lib/EnsEMBL/REST/Model/ga4gh/Beacon.pm
@@ -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',
diff --git a/root/documentation/vep.conf b/root/documentation/vep.conf
index 8e09b648..047111f7 100644
--- a/root/documentation/vep.conf
+++ b/root/documentation/vep.conf
@@ -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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