Added --ignore-overlaps to disable read-pair overlap detection.

drpatelh · Dec 4, 2020 · 46d97f5 · 46d97f5
1 parent 8178093
commit 46d97f5
Showing 1 changed file with 1 addition and 0 deletions.
diff --git a/main.nf b/main.nf
@@ -1287,6 +1287,7 @@ process SAMTOOLS_MPILEUP {
     """
     samtools mpileup \\
         --count-orphans \\
+        --ignore-overlaps \\
         --no-BAQ \\
         --max-depth $params.mpileup_depth \\
         --fasta-ref $fasta \\