I have made the mistake of using the default compression level for ApplyBQSR and now I have terabytes of wasted space in my project bam files. The recalibrated files take up twice the disk space in comparison to the original files. Is there a way to change the existing compression level of the base quality score recalibrated bam files?
It does not make sense to keep multiple versions of the same sample or run our analyses on different bam files (recalibrated vs non-recalibrated), so we want to keep the BQSR files for long term storage and future use. This is a massive waste of space.
I'm am experimenting with running ApplyBQSR with "--java-options Dsamjdk.compression_level=5" but I would really like to change the compression level of the existing bam files. Is this possible?
Please sign in to leave a comment.