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I/O to import genotype data from standard file formats #2

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quattro opened this issue Jun 14, 2023 · 1 comment
Open
3 of 4 tasks

I/O to import genotype data from standard file formats #2

quattro opened this issue Jun 14, 2023 · 1 comment
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enhancement New feature or request

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@quattro
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quattro commented Jun 14, 2023

Catch-all for implementing I/O routines to load genotype data from standardized data formats. Namely,

  • PLINK formatted data
  • PLINK2 formatted data
  • VCF (gzip VCF) formatted data
  • BGEN formatted data

We can leverage existing libraries as dependencies to load in these data when possible, but might require some custom code to avoid materializing entire dense genotype vectors/matrices in memory.

@quattro quattro added the enhancement New feature or request label Jun 14, 2023
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quattro commented Jan 31, 2024

Let's use some of the sparse readers implemented here: https://github.com/fastlmm/bed-reader

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