Hello everyone!

snpeff was updated to 5.0:

• includes more genomes (has even SARS COVID2);
• databases moved to the Microsoft cloud;

Changes in bcbio:
https://github.com/chapmanb/cloudbiolinux/blob/master/contrib/flavor/ngs_pipeline_minimal/packages-conda.yaml#L125
#3569

Update with
bcbio_nextgen.py -u development --tools --genomes hg38

To check:

$ snpEff -version
$ ls [bcbio]/genomes/Hsapiens/snpeff/GRCh38.99

Please let me know if you experience any issues with the updated snpeff.

SN