Question: plink 1.9 PED to VCF, SNPs differ on input and output files
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5.3 years ago by
stolarek.ir650 wrote:


I am using plink v 1.9 to convert my ped file to vcf with command:

./plink --ped file.ped --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:

VCF file:

1    50798494    SNP_A-4278605    C    .

BIM file:

1       SNP_A-4278605   0       50798494        T       C

Has anyone encountered this?

snp plink • 3.3k views
ADD COMMENTlink written 5.3 years ago by stolarek.ir650
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