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fcGENE error during conversion from .ped to .gen

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.
imputation fcgene
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updated by Ram Ram • written by pifferdavide pifferdavide

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

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written by chrchang523 chrchang523

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