Dosage data single probability to PLINK format

Question

[smb2174]

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

thanks!

[chenhongyao6694]

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.

Answer 1

[chrchang523]

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.

[yulin1988320]

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.