plink 1.9 PED to VCF, SNPs differ on input and output files

Question

[stolarek.ir]

Hi,

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 turns out some SNPs in the vcf file differ from those in bim file:

VCF file:

1    50798494    SNP_A-4278605    C    .

BIM file:

1       SNP_A-4278605   0       50798494        T       C

Has anyone encountered this?