【计算Nei遗传距离】

报错

Warning message:
In adegenet::df2genind(t(x), sep = sep, ...) :
  Markers with no scored alleles have been removed

原因：

直接用plink转换为VCF，丢失了等位基因分型（REF    ALT）

 （plink编码的规则）

而其它的不识别这样的规则，同样用plink转换为vcf时，会有这样的提示。

Warning: Underscore(s) present in sample IDs.
--recode vcf to test.vcf ... done.
Warning: At least one VCF allele code violates the official specification;
other tools may not accept the file.  (Valid codes must either start with a
'<', only contain characters in {A,C,G,T,N,a,c,g,t,n}, be an isolated '*', or
represent a breakend.)
 

解决办法：缺失替换为*