Set maximum population frequency to 1%

LUMC · Oct 28, 2024 · 822b97a · 822b97a
1 parent a28df77
commit 822b97a
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Showing 4 changed files with 8 additions and 4 deletions.
diff --git 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
@@ -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
@@ -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
@@ -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: