fcGENE error during conversion from .ped to .gen

Question

[pifferdavide]

I converted .vcf genotype file to .ped using plink like so:

./plink --vcf hgdp_wgs.20190516.full.chr22.vcf.gz --maf 0.01 --recode --out hgdp_chr22

When I try to convert a .ped file to impute format

./fcgene --ped hgdp_22.ped --map hgdp_22.map --oformat impute --out hgdp_22_impute

I get the following error:

Reading  ped file: "hgdp_22.ped":
ERROR: Problem in reading  SNP rs1245595155 in line1. The SNP has genotype [ TA ] and [TAA],  each should be only one characters long.

[chrchang523]

You can just use plink "--recode oxford" for this. With plink 2.0, this also works with dosage data.

[pifferdavide]

Thanks, this worked!