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2 hours ago by

test.vcf:

##fileformat=VCFv4.0
#CHROM  POS ID  REF ALT QUAL    FILTER  INFO    FORMAT  NA00001 NA00002 NA00003 NA00004 NA00005
19  111 .   A   C   .   .   .   GT  1/1 1/1 1/1 0/1 0/1

I run:

plink 
--vcf test.vcf 
--out test

plink 
--bfile test 
--freq 
--out test

my .bim file

19  .   0   111 C   A

my .frq file

 CHR  SNP   A1   A2          MAF  NCHROBS
  19    .    A    C          0.2       10

If the sixth column of the .bim file is supposed to be A2, why does it not agree with the .frq file?



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