Question: plink 1.9 PED to VCF, SNPs differ on input and output files
0
gravatar for stolarek.ir
4.0 years ago by
stolarek.ir600
Poland
stolarek.ir600 wrote:

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 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 • 2.5k views
ADD COMMENTlink written 4.0 years ago by stolarek.ir600
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1977 users visited in the last hour