Storing FASTQ as unaligned CRAM

I was updating my BAM to CRAM post spurred on by a recent comment and then I wondered whether I could store my FASTQ files as unaligned CRAM files to save space. I thought it wouldn’t be possible because the reads are unaligned and therefore we can’t make use of a reference to save space…

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BAM to CRAM

Updated 2022 January 20th. As pointed out by Colin, converting a BAM file to CRAM is simply one command: Of note is that the reference file used to produce the BAM file is required and is used as an argument for the -T option. As for why we should convert from BAM to CRAM, the…

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