From d6c6fbbf4d1711db5948acc8c12f3a288dac767a Mon Sep 17 00:00:00 2001
From: Brandi Cantarel <brandi.cantarel@utsouthwestern.edu>
Date: Mon, 6 May 2019 20:40:09 -0500
Subject: [PATCH] update markdups
---
alignment/markdups.sh | 3 ---
1 file changed, 3 deletions(-)
diff --git a/alignment/markdups.sh b/alignment/markdups.sh
index 9a5eb6b..5687a5d 100644
--- a/alignment/markdups.sh
+++ b/alignment/markdups.sh
@@ -42,9 +42,6 @@ then
sambamba markdup -t $SLURM_CPUS_ON_NODE ${sbam} ${pair_id}.dedup.bam
elif [ $algo == 'samtools' ]
then
- samtools sort -n -@ $SLURM_CPUS_ON_NODE -o nsort.bam ${sbam}
- samtools fixmate -c --output-fmt BAM -m -@ $SLURM_CPUS_ON_NODE nsort.bam fix.bam
- samtools sort -n -@ $SLURM_CPUS_ON_NODE -o sort.bam fix.bam
samtools markdup -s --output-fmt BAM -@ $SLURM_CPUS_ON_NODE sort.bam ${pair_id}.dedup.bam
elif [ $algo == 'picard' ]
then
--
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