We have developed our own tool for compression, which saves ~70% while creating "regular" BAM files. But we are seeing all these new formats that are space economic - but I want to hear from people who are actually using them if they have hidden caveats and what performance I should be expecting.
Eitan Rubin
I developed my own (rejected from "bioinformatics"). Simply remove extra or computable fields, cap the maximal quality you care about (we used 23) and use the '=' format, and you will save ~80% of the disk space.
The result is still BAM, and many programs will work with it without "decompression".
I can share the tool if you want.
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