Question: Dosage data single probability to PLINK format
gravatar for smb2174
4.1 years ago by
smb21740 wrote:

Hi All,

I have imputed dosage file with just one probability any software that can convert it to PLINK ped/map files? Unfortunately gtool only take the 3 probabilities dosage files


imputation • 3.0k views
ADD COMMENTlink modified 2.9 years ago by chrchang5237.6k • written 4.1 years ago by smb21740

I meet the same problem as you,and I wonder that if you have solved the problem.Which software did you use to convert the dosage file to PLINK files? thanks.

ADD REPLYlink written 2.9 years ago by chenhongyao66940
gravatar for chrchang523
2.9 years ago by
United States
chrchang5237.6k wrote:
  1. Use plink 2.0’s —import-dosage and —make-bed flags to generate plink bed/bim/fam files. —hard-call-threshold can be used to control which dosage values get rounded to the nearest integer vs. converted to a missing call.
  2. plink 1.x’s —recode command converts bed/bim/fam to ped/map.
ADD COMMENTlink written 2.9 years ago by chrchang5237.6k

I searched this question 8 months ago, and did not get a satisfied result. I used the Beagle4.0 utilities to generate vcf first and then to plink format. This way is much better. Thanks again, Christ.

ADD REPLYlink written 2.4 years ago by yulin198832020
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