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Commit 4db3ad56 authored by Brandi Cantarel's avatar Brandi Cantarel
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typo fgbio

parent 99628b0d
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alignment/markdups.sh
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...@@ -56,8 +56,8 @@ elif [ $algo == 'fgbio_umi' ] ...@@ -56,8 +56,8 @@ elif [ $algo == 'fgbio_umi' ]
then then
module load fgbio bwa/intel/0.7.15 module load fgbio bwa/intel/0.7.15
samtools index -@ $SLURM_CPUS_ON_NODE ${sbam} 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 --tmp-dir ./ GroupReadsByUmi -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 ./ CallMolecularConsensusReads -i ${pair_id}.group.bam -p consensus -M 1 -o ${pair_id}.consensus.bam -S ':none:'
samtools index ${pair_id}.consensus.bam samtools index ${pair_id}.consensus.bam
samtools fastq -1 ${pair_id}.consensus.R1.fastq -2 ${pair_id}.consensus.R2.fastq ${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 gzip ${pair_id}.consensus.R1.fastq
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