Bug Bulletin: we have identified a bug that affects indexing when producing gzipped VCFs. This will be fixed in the upcoming 3.2 release; in the meantime you need to reindex gzipped VCFs using Tabix.

Adjusting BAM compression level

mjlarsenmjlarsen Posts: 2Member

Is it possible to adjust the compression level of the BAM-files (like i picard etc). To optimize speed/disk long term disk usage, this would be advantageous when producing temporary/final BAM files, e.g. using the indelrealigner and printreads tools, respectively.

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