From 822b97a5aff752179122afd8a680121a1ee24536 Mon Sep 17 00:00:00 2001
From: Redmar van den Berg <RedmarvandenBerg@lumc.nl>
Date: Mon, 28 Oct 2024 14:40:50 +0100
Subject: [PATCH] Set maximum population frequency to 1%

---
 CHANGELOG.rst                 | 5 +++++
 common.smk                    | 2 +-
 docs/source/conf.py           | 2 +-
 includes/snv-indels/Snakefile | 3 +--
 4 files changed, 8 insertions(+), 4 deletions(-)

diff --git a/CHANGELOG.rst b/CHANGELOG.rst
index 43300fa..439b5c6 100644
--- a/CHANGELOG.rst
+++ b/CHANGELOG.rst
@@ -7,6 +7,11 @@ Changelog
 ..  This document is user facing. Please word the changes in such a way
 .. that users understand how the changes affect the new version.
 
+**********
+v2.1.2
+**********
+* Set the maximum population frequency to 1%. This was accidentally set to 5% in v2.1.1
+
 **********
 v2.1.1
 **********
diff --git a/common.smk b/common.smk
index e9d3843..7a4e35a 100644
--- a/common.smk
+++ b/common.smk
@@ -17,4 +17,4 @@ containers = {
 }
 
 # The version of HAMLET
-PIPELINE_VERSION = "v2.1.1"
+PIPELINE_VERSION = "v2.1.2"
diff --git a/docs/source/conf.py b/docs/source/conf.py
index 708b57b..269bb68 100644
--- a/docs/source/conf.py
+++ b/docs/source/conf.py
@@ -6,7 +6,7 @@
 copyright = '2018, LUMC'
 author = 'Wibowo Arindrarto, Redmar van den Berg, Xiaoyun Liu'
 
-release = "v2.1.1"
+release = "v2.1.2"
 version = '.'.join(release.split('.')[0:2])
 
 # -- General configuration
diff --git a/includes/snv-indels/Snakefile b/includes/snv-indels/Snakefile
index ee91824..9a3b6c3 100644
--- a/includes/snv-indels/Snakefile
+++ b/includes/snv-indels/Snakefile
@@ -322,7 +322,6 @@ rule annotate_vars:
             if config.get("vep_cache")
             else ""
         ),
-        max_pop_af=0.01,
     output:
         vep="{sample}/snv-indels/{sample}.vep.txt.gz",
         stats="{sample}/snv-indels/{sample}.vep_stats.txt",
@@ -382,7 +381,7 @@ rule filter_vep:
         vep_consequences=config["vep_include_consequence"],
         blacklist=f"--blacklist {config['blacklist']}" if "blacklist" in config else "",
         population="gnomade",
-        max_pop_af=0.05,
+        max_pop_af=0.01,
     output:
         filtered="{sample}/snv-indels/{sample}.vep.filtered.txt.gz",
     log: