Genotype & Variant formats binary mode

[Ivan Kizema]

Hello,

The Genotype & Variant formats are slightly different in text and binary mode. In general, the information remains the same and only the format changes. But, in .BIM record (Genotype & Variant format binary mode), there are Reference allele and Alternate allele columns. We can't find this information in Genotype & Variant format text mode (.PED and .MAP Records). Can you please provide some information on how those two columns are calculated ?

Many Thanks,
Ivan

[Christopher Chang]

By default, the 5th column in the .bim ("A1") is the minor allele and the 6th column ("A2") is the major allele.  This can be changed with the --a1-allele and --a2-allele flags.

When exporting a VCF file, the reference allele is set to A2.  (Since PLINK normally resets the major allele to A2 on *every* run, it is frequently necessary to use the --a2-allele flag when exporting a VCF.)