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?
