Plink v2.0 does not produce a Z-compressed file (.zst)
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Entering edit mode
9 months ago
giusdalt95 ▴ 10

Good morning, I would like to convert a merged VCF in a Plink compressed format (.pgen, .psam and .pvar files), so I run

plink2 --vcf MyMerged.vcf.gz --make-pgen --zst-level 3 --out MySamples

It basically works, as it produces such files:

ls -1 MySamples
MySamples.pgen
MySamples.psam
MySamples.pvar

Nevertheless, I'd need a "MySamples.pgen.zst" file in order to perform some operations, e.g. visualize the resulting matrix in R (see here for more details). Could anybody help me out? Thanks in advance

Plink v2.0 VCF • 238 views
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