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Question: fcGENE error during conversion from .ped to .gen
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gravatar for pifferdavide
7 months ago by
pifferdavide • 100
Italy
pifferdavide • 100 wrote:

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 format conversion fcgene • 237 views
ADD COMMENT • link •
written 7 months ago by pifferdavide • 100
1

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

ADD REPLY • link written 7 months ago by chrchang523 ♦ 6.5k

Thanks, this worked!

ADD REPLY • link modified 7 months ago • written 7 months ago by pifferdavide • 100
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