Generally, I use
index BAM files. Samtools works also with BGZF compressed SAM but not with plain ones.
I have terabytes of plain SAMs at the moment and I would love to avoid compression/conversion. I have all the data in several external HD and I am not allowed to delete the original SAM files. I would need much more space than I have now to also store the BAM files.
So, I was wondering if there is a way to avoid it. Is there some tool/trick to sort and index uncompressed SAM files, without converting them to BAM or compressing them?