From 2f09a2d68edaaa32e683c75ab2580986620652a3 Mon Sep 17 00:00:00 2001
From: Brandi Cantarel <brandi.cantarel@utsouthwestern.edu>
Date: Wed, 22 May 2019 09:23:32 -0500
Subject: [PATCH] removing FixMate Line
---
alignment/rnaseqalign.sh | 2 --
1 file changed, 2 deletions(-)
diff --git a/alignment/rnaseqalign.sh b/alignment/rnaseqalign.sh
index 606af0a..963143f 100644
--- a/alignment/rnaseqalign.sh
+++ b/alignment/rnaseqalign.sh
@@ -70,8 +70,6 @@ else
samtools view -1 --threads $SLURM_CPUS_ON_NODE -o output.bam out.sam
fi
samtools sort -@ $SLURM_CPUS_ON_NODE -O BAM -o ${pair_id}.bam output.bam
- java -jar $PICARD/picard.jar FixMateInformation ASSUME_SORTED=TRUE SORT_ORDER=coordinate ADD_MATE_CIGAR=TRUE I=output.nsort.bam O=${pair_id}.bam
-
fi
samtools index -@ $SLURM_CPUS_ON_NODE ${pair_id}.bam
--
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