Genotype Data in PLINK
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4 weeks ago

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 • 454 views
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4 weeks ago
Sam ★ 3.5k

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

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

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You mean dosage in terms of imputation? Think it does https://www.cog-genomics.org/plink/2.0/input#pgen

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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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For that, you can do it with --recode in plink 1.9, though the results will be plain text format, not PLINK file format

https://www.cog-genomics.org/plink/1.9/data#recode

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

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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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