MergeAllBamFilesWithBash.sh
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find $BAM_DIR -name '*.bam' | { read firstbam samtools view -h "$firstbam" while read bam; do samtools view "$bam" done } | samtools view -ubS - | samtools sort -o merged.bam - samtools index merged.bam ls -l merged.bam merged.bam.bai