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Genotype Data in PLINK

Hello,

In PLINK file formats can we represent genotype data as allelic dosage. Or is that a must to represent them as biallelic?

Thank You

genotype plink
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updated by Sam Sam • written by carlstat123 • carlstat123

1 answer

Depends. Think PLINK-2.0 has a new format pgen which can account for allelic dosage

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written by Sam Sam

But .pgen file is a binary file right? How can we make it as alelic dosage?

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written by carlstat123 • carlstat123

I mean if genotype is 00 then allelic dosage is 0, 10 or 01 it is 1 and 11 allelic dosage is 2.

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written by carlstat123 • carlstat123

But --recode creates .ped+ .fam files right? So can not we consider it as PLINK file formats?

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written by carlstat123 • carlstat123

PLINK 1.9's core file format is .bed + .bim + .fam. Any other format is automatically converted by PLINK 1.9 to a .bed + .bim + .fam temporary fileset. This conversion is less efficient for .ped than for VCF, so it is fair to say that .ped has been less supported by PLINK than VCF since 2014, despite the historical origin of .ped.

No PLINK 2.0 build over the last four years can either read or write .ped.

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written by chrchang523 chrchang523

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