Commits (2)
......@@ -57,8 +57,8 @@ elif [ $algo == 'fgbio_umi' ]
then
module load fgbio bwa/intel/0.7.15
samtools index -@ $SLURM_CPUS_ON_NODE ${sbam}
fgbio -Djava.io.tmpdir=./ GroupReadsByUmi -s identity -i ${sbam} -o ${pair_id}.group.bam -e 0 -m 0
fgbio -Djava.io.tmpdir=./ CallMolecularConsensusReads -i ${pair_id}.group.bam -p consensus -M 1 -o ${pair_id}.consensus.bam -S ':none:'
fgbio GroupReadsByUmi -s identity -i ${sbam} -o ${pair_id}.group.bam -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
gzip ${pair_id}.consensus.R1.fastq
......