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Compressing gVCFs in GATK4

jphekmanjphekman Broad InstituteMember

Hi all. Our team has been gzipping gVCFs for medium term storage, but has found it quite burdensome to have to periodically ungzip them to joint genotype them (the space requirements for our large numbers of files are challenging). We are seeking a solution where we can joint genotype gzipped or otherwise compressed gVCFs.

In face to face meetings with GATK team members, we were told that in GATK4, we can ask earlier steps in the pipeline (HaplotypeCaller I'm guessing?) to gzip gVCFs, and then joint genotyping can run on those GATK-compressed gVCFs without us having to unzip them. We are all for that!

I have been looking for documentation about how exactly this works and failed to find it. Help?

Best,
Jessica

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