Question: fcGENE error during conversion from .ped to .gen
0
gravatar for pifferdavide
10 weeks ago by
pifferdavide100
Italy
pifferdavide100 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.

ADD COMMENTlink written 10 weeks ago by pifferdavide100
1

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

ADD REPLYlink written 10 weeks ago by chrchang5235.5k

Thanks, this worked!

ADD REPLYlink modified 10 weeks ago • written 10 weeks ago by pifferdavide100
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: 1122 users visited in the last hour