Apr 21, 2021
On considering the .bim files at these problem snps for each population example allele codes are as follows:
Pop1: rs1000000 A G
Pop2: rs1000000 T C
Pop3: rs1000000 A G
This indicates to me that Pop2 has undergone strand flip.
PLINK gives you a list of SNPs who need to be flipped (???.missnp). You need to flip these SNPs :
Step 1 - First merge: plink --file fA --merge-list allfiles.txt --make-bed --out mynewdata
Step 2 - Flip SNPs: plink --file fA --flip mynewdata.missnp --make-bed --out mynewdata2
Step 3 - New merge: plink --bfile mynewdata2 --merge-list allfiles.txt --make-bed --out mynewdata3
After the second merge, if you still have a bug about the strand, those SNPs are probably triallelic.