what is the difference between plink1.9 and plink2 in difining reference allele

[Sean]

When read the sample bed file, Plink 1.9 shows two alleles in A1 and A2. Plink 2.0 shows two alleles in Ref and Alt.  Here, A1 and Ref are the same?

How does plink1.9 and plink2.0 define reference level of a SNP in linear model? Always define minor frequent allele as 0 (the other as 1)?

[Christopher Chang]

1. No, in Plink 1.x, A1 is usually the minor allele and A2 the major allele.  The allele matching the reference genome ("Ref") is more likely to be major/A2, but they won't always match.

2. By default, plink 2.0 --glm does the same thing as plink 1.9 --linear: the genotype column contains the number of copies of the minor allele.  However, you can make it include alternate-allele counts instead; see the 'omit-ref' modifier at https://www.cog-genomics.org/plink/2.0/assoc#glm .