On the PacBio Revio instrument we are sorting our hifi_reads.bam files with samtools sort -M -R to save disk space and improve file transfer time. The SO:coordinate results in a lot of confusion, as users think that the file is already aligned.
I could override the sort order using a new option and set it to unknown in my use case. If I were to implement this, would you accept such solution or do you have a different idea?
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