I am using plink v 1.9 to convert my ped file to vcf with command:
./plink --ped file.ped --map file.map --recode vcf --out ped_to_vcf
(ped file was obtained by running standard plink command on .bim/.bed/.fam files)
As it turnes out some SNPs in the vcf file differ from those in bim file:
1 50798494 SNP_A-4278605 C .
1 SNP_A-4278605 0 50798494 T C
Has anyone encountered this?