From ddbcd917d9b301a9e1b4ce6f1f5f853dda1fdff7 Mon Sep 17 00:00:00 2001
From: Brandi Cantarel <brandi.cantarel@utsouthwestern.edu>
Date: Mon, 11 Mar 2019 10:38:50 -0500
Subject: [PATCH] add umihist to alignment
---
alignment/markdups.sh | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/alignment/markdups.sh b/alignment/markdups.sh
index b794b25..1ff03f9 100644
--- a/alignment/markdups.sh
+++ b/alignment/markdups.sh
@@ -57,7 +57,7 @@ elif [ $algo == 'fgbio_umi' ]
then
module load fgbio bwa/intel/0.7.15
samtools index -@ $SLURM_CPUS_ON_NODE ${sbam}
- fgbio GroupReadsByUmi -s identity -i ${sbam} -o ${pair_id}.group.bam -e 0 -m 0
+ 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 -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
--
GitLab