From 3cc18126de3bbde8920f2a9164953c80340f2472 Mon Sep 17 00:00:00 2001
From: Syed Nakib Hossain <snhossain@ebi.ac.uk>
Date: Wed, 13 Dec 2023 14:00:58 +0000
Subject: [PATCH] Add examples for CADD options
---
root/documentation/vep.conf | 6 ++++++
1 file changed, 6 insertions(+)
diff --git a/root/documentation/vep.conf b/root/documentation/vep.conf
index 3ead2aad..7895aba0 100644
--- a/root/documentation/vep.conf
+++ b/root/documentation/vep.conf
@@ -298,6 +298,7 @@
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>)
default=0
+ example=snv_indels,<wbr>1
</CADD>
<OpenTargets>
type=Boolean
@@ -631,6 +632,7 @@
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>)
default=0
+ example=snv_indels,<wbr>1
</CADD>
<OpenTargets>
type=Boolean
@@ -952,6 +954,7 @@
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>)
default=0
+ example=snv_indels,<wbr>1
</CADD>
<OpenTargets>
type=Boolean
@@ -1267,6 +1270,7 @@
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>)
default=0
+ example=snv_indels,<wbr>1
</CADD>
<OpenTargets>
type=Boolean
@@ -1593,6 +1597,7 @@
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>)
default=0
+ example=snv_indels,<wbr>1
</CADD>
<OpenTargets>
type=Boolean
@@ -1927,6 +1932,7 @@
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>)
default=0
+ example=snv_indels,<wbr>1
</CADD>
<OpenTargets>
type=Boolean
--
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