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Add support for plink2 binary format dosage data (pgen) #253

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sritchie73 opened this issue Aug 9, 2021 · 3 comments
Open

Add support for plink2 binary format dosage data (pgen) #253

sritchie73 opened this issue Aug 9, 2021 · 3 comments

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@sritchie73
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E.g. via a snp_readPgen() function analogous to snp_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):

  • 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.
@privefl
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privefl commented Aug 9, 2021

Please see #176 (comment).

@privefl
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privefl commented Sep 2, 2021

If anyone is willing to help implementing this, please discuss here.

@privefl privefl changed the title Feature request: support for plink2 binary format dosage data Support for plink2 binary format dosage data Mar 1, 2022
@privefl privefl changed the title Support for plink2 binary format dosage data Add support for plink2 binary format dosage data Mar 1, 2022
@privefl privefl changed the title Add support for plink2 binary format dosage data Add support for plink2 binary format dosage data (pgen) Mar 1, 2022
@privefl
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privefl commented Nov 21, 2022

In the meantime, you can have a look at the last point of https://privefl.github.io/bigsnpr-extdoc/inputs-and-formats.html#getting-FBM for a workaround.

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