对genotype的等位型进行计数，需要用到以下参数：
--freq Allele frequencies
--countsModifies --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 '--freq counts'. Valid input for --read-freq.
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