From 4db3ad5670f113a1c3a9aa9d09374ba81ef8d69d Mon Sep 17 00:00:00 2001
From: Brandi Cantarel <brandi.cantarel@utsouthwestern.edu>
Date: Mon, 18 Nov 2019 08:38:17 -0600
Subject: [PATCH] typo fgbio
---
alignment/markdups.sh | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/alignment/markdups.sh b/alignment/markdups.sh
index 565fac7..4b897a2 100644
--- a/alignment/markdups.sh
+++ b/alignment/markdups.sh
@@ -56,8 +56,8 @@ elif [ $algo == 'fgbio_umi' ]
then
module load fgbio bwa/intel/0.7.15
samtools index -@ $SLURM_CPUS_ON_NODE ${sbam}
- fgbio GroupReadsByUmi --tmp-dir ./ -s identity -i ${sbam} -o ${pair_id}.group.bam --family-size-histogram ${pair_id}.umihist.txt -e 0 -m 0
- fgbio CallMolecularConsensusReads --tmp-dir ./ -i ${pair_id}.group.bam -p consensus -M 1 -o ${pair_id}.consensus.bam -S ':none:'
+ fgbio --tmp-dir ./ GroupReadsByUmi -s identity -i ${sbam} -o ${pair_id}.group.bam --family-size-histogram ${pair_id}.umihist.txt -e 0 -m 0
+ fgbio --tmp-dir ./ CallMolecularConsensusReads -i ${pair_id}.group.bam -p consensus -M 1 -o ${pair_id}.consensus.bam -S ':none:'
samtools index ${pair_id}.consensus.bam
samtools fastq -1 ${pair_id}.consensus.R1.fastq -2 ${pair_id}.consensus.R2.fastq ${pair_id}.consensus.bam
gzip ${pair_id}.consensus.R1.fastq
--
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