plink重编码为raw文件时以reference allele计数

--recode creates a new text fileset, after applying sample/variant filters and other operations. By default, the fileset includes a .ped and a .map file, readable with --file. Note that the .ped+.map format is NOT a native file format for PLINK 1.9 — any operation on it requires inefficient conversion to .bed+.bim+.fam — and should almost never be used in new scripts. VCF is usually a better choice when you must convert to text.
The 'AD' modifier causes an additive (0/1/2) + dominant (het = 1, otherwise 0) component file, suitable for loading from R, to be generated. 'A' is the same, except without the dominance component.

• By default, A1 alleles are counted; this can be customized with --recode-allele. --recode-allele's input file should have variant IDs in the first column and allele IDs in the second.
• By default, the header line for .raw files only names the counted alleles. To include the alternate allele codes as well, add the 'include-alt' modifier.
• Haploid additive components are 0/2-valued instead of 0/1-valued, to maintain a consistent scale on the X chromosome.

--recode A 转成012的raw格式的时候，默认是A1 alleles are counted，即最小等位基因用来计数。

如果想变成以reference allele计数，需要使用--recode-allele自定义需要计数的allele