对genotype的等位型进行计数，需要用到以下参数：

--freq Allele frequencies

--counts Modifies --freq to report actual allele counts

具体用法如下命令：

/plink-1.07-x86_64/plink --freq --counts --noweb --bfile file  --make-bed --out file

　

.frq.count (basic allele count report)

Produced by ''. Valid input for .

A text file with a header line, and then one line per variant with the following seven fields:

CHR	Chromosome code
SNP	Variant identifier
A1	Allele 1 (usually minor)
A2	Allele 2 (usually major)
C1	Allele 1 count
C2	Allele 2 count
G0	Missing genotype count (so C1 + C2 + 2 * G0 is constant on autosomal variants)

 

注意：这里用到的是plink的1.07版本，如果是1.9或者2.0版本，则命令可能会有些许的改动，具体参考官网。

参考：http://zzz.bwh.harvard.edu/plink/reference.shtml