Overview

samtools fastq [options] in.bam samtools fasta [options] in.bam Converts a BAM or CRAM into either FASTQ or FASTA format depending on the command invoked. The files will be automatically compressed if the file names have a .gz or .bgzf extension. The input to this program must be collated by name. Use samtools collate or samtools sort -n to ensure this.

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