Allele1 allele2 what do they represent?
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Peiyuan Zhu
Jul 11, 2025, 12:00:42 AMJul 11
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For allele1 and allele2, which one is reference and which one is alternative? Is the dosage number the copies of reference allele or alternative allele?
Christopher Chang
Jul 12, 2025, 11:52:04 AMJul 12
to plink2-users
https://www.cog-genomics.org/plink/1.9/formats#bim
Use plink2 --pfile/--make-pgen, instead of --bfile/--make-bed, if you want to easily keep REF/ALT alleles straight.
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