diff --git a/alignment/markdups.sh b/alignment/markdups.sh index b794b25c4e26a1691252dce8ea5cae323f621b8e..1ff03f909d7c1b327e5c03b6e81db747386c9e42 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