From 1c1e036ee10f713f8a56f026b14499e2768d4f03 Mon Sep 17 00:00:00 2001
From: Venkat Malladi <venkat.malladi@utsouthwestern.edu>
Date: Sat, 12 Jan 2019 00:24:58 -0600
Subject: [PATCH] Fix filter reads output.
---
workflow/scripts/map_qc.py | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/workflow/scripts/map_qc.py b/workflow/scripts/map_qc.py
index 031034a..920e009 100644
--- a/workflow/scripts/map_qc.py
+++ b/workflow/scripts/map_qc.py
@@ -153,7 +153,7 @@ def dedup_mapped(bam, bam_basename, paired):
'''Use sambamba and samtools to remove duplicates.'''
# Markduplicates
- dup_file_qc_filename = bam_basename + ".dup.qc"
+ dup_file_qc_filename = bam_basename + ".dedup.qc"
tmp_dup_mark_filename = bam_basename + ".dupmark.bam"
sambamba_params = "--hash-table-size=17592186044416" + \
" --overflow-list-size=20000000 --io-buffer-size=256"
--
GitLab