Remove default filters in mpileup as well...

mpieva · Nov 19, 2024 · b418acb · b418acb
1 parent 21d24c1
commit b418acb
Showing 1 changed file with 1 addition and 1 deletion.
diff --git a/conf/process.config b/conf/process.config
@@ -144,7 +144,7 @@ process {
     }
 
     withName:"SAMTOOLS_MPILEUP" {
-        ext.args = "--output-BP-5 --no-output-ends --no-output-ins --no-output-del --no-output-ins --no-output-del --min-BQ 0  -R"
+        ext.args = "--output-BP-5 --no-output-ends --no-output-ins --no-output-del --no-output-ins --no-output-del --min-BQ 0  -R --ff 0"
         publishDir = [
             [
                 path: "${outdir}/out",