From 0ccf418d0e2b2bf69c8cc0533998e6a41ab97245 Mon Sep 17 00:00:00 2001
From: Brandi Cantarel <brandi.cantarel@utsouthwestern.edu>
Date: Fri, 10 Nov 2017 16:06:59 -0600
Subject: [PATCH] typo markdups
---
alignment/markdups.sh | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/alignment/markdups.sh b/alignment/markdups.sh
index 5158e78..7bf4709 100644
--- a/alignment/markdups.sh
+++ b/alignment/markdups.sh
@@ -48,7 +48,7 @@ then
samtools markdup -s --output-fmt BAM -@ $SLURM_CPUS_ON_NODE sort.bam ${pair_id}.dedup.bam
elif [ $algo == 'picard' ]
then
- java -Djava.io.tmpdir=./ -Xmx4g -jar $PICARD/picard.jar MarkDuplicates I=${sbam} O=${prefix}.dedup.bam M=${pair_id}.dedup.stat.txt
+ java -Djava.io.tmpdir=./ -Xmx4g -jar $PICARD/picard.jar MarkDuplicates I=${sbam} O=${pair_id}.dedup.bam M=${pair_id}.dedup.stat.txt
elif [ $algo == 'picard_umi' ]
then
java -Djava.io.tmpdir=./ -Xmx4g -jar $PICARD/picard.jar MarkDuplicates BARCODE_TAG=RX I=${sbam} O=${pair_id}.dedup.bam M=${pair_id}.dedup.stat.txt
@@ -67,5 +67,5 @@ then
bwa mem -M -C -t 2 -R '@RG\tID:${pair_id}\tLB:tx\tPL:illumina\tPU:barcode\tSM:${pair_id}' /project/shared/bicf_workflow_ref/GRCh38/genome.fa ${pair_id}.consensus.R1.fastq.gz ${pair_id}.consensus.R2.fastq.gz | samtools view -1 - > ${pair_id}.consensus.bam
samtools sort --threads 10 -o ${pair_id}.dedup.bam ${pair_id}.consensus.bam
else
- cp ${sbam} ${prefix}.dedup.bam
+ cp ${sbam} ${pair_id}.dedup.bam
fi
--
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