added dont-use-soft-clipped-bases to GATK to imporve variant calling …

…for amplicon sequencing approach
UMCUGenetics · Mar 8, 2024 · c2f14ce · c2f14ce
1 parent edd4797
commit c2f14ce
Showing 1 changed file with 1 addition and 1 deletion.
diff --git a/conf/modules.config b/conf/modules.config
@@ -54,7 +54,7 @@ process {
         memory = { 10.GB * task.attempt }
         time = { 10.m * task.attempt }
 
-        ext.args = "--emit-ref-confidence BP_RESOLUTION"
+        ext.args = "--emit-ref-confidence BP_RESOLUTION --dont-use-soft-clipped-bases "
         ext.prefix = { "${meta.id}.g" }
     }