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Data are stored as probabilistic dosages, rather than hard call genotypes (i.e. floating point between 0 and 2)
There's less missing data compared to the hard call genotype data
It's more compact than plink1 binary format (e.g. the full UKB dataset takes 2.4TB in pgen format, and 11TB in the bed format).
Disavantages:
The plink2 binary format is still in draft specification so may be subject to change. That being said, I've been working with pgen files for a few years now with numerous updates to plink2 and there have been no such changes in that time, so I gather the format is relatively mature.
The text was updated successfully, but these errors were encountered:
E.g. via a
snp_readPgen()
function analogous tosnp_readBed()
.The plink2 binary format (https://www.cog-genomics.org/plink/2.0/input#pgen) has several advantages over the plink1 binary format (bed/bim/fam):
Disavantages:
The text was updated successfully, but these errors were encountered: