I've released an update to BOLT-LMM (v2.4.1) that adds support for BGEN files that use Zstandard compression (e.g., the recent TOPMed and GEL imputation data sets and the WES genotype calls).
If the version of BOLT-LMM included with Swiss Army Knife could be updated in the next SAK release, that would be great.
For now, the new release is available here:
https://storage.googleapis.com/broad-alkesgroup-public/BOLT-LMM/downloads/BOLT-LMM_v2.4.1.tar.gz
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Thanks @Po-Ru Loh? ! I will let the product team knows right away.
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