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