The front line support team will be unavailable to answer questions until May 27th 2019 as we are celebrating Memorial Day. We will be back soon after. Thank you for your patience and we apologize for any inconvenience!
CRAM support timeline
With the recent release of improvements to sequencing my poor disks are threatened with an influx of more data than ever and I've been trying to figure out ways of reducing the amount of space each sample takes up on our fast compute disks (as well as the time it has to spend there). One of the approaches I am exploring is the use of CRAM (in lossless mode initially) in place of BAM as our primary binary reads format as it seems likely to become the preferred format of the ENA/EGA the SRA where we archive our BAMs.
A samtools version that will support CRAM will be released in a few weeks; CRAMtools hacks support into Picard but at the moment I'm stuck using BAM for steps with involve GATK. I was wondering if this was likely to change in the near future, if so whether it's likely to be weeks, months or undefined as yet wish list?