Hi,
I am wondering how can I convert the imputed genotype data from Beagle (*.dosage.gz) to plink bed format? It is not in *.bgl format and I cannot convert the data using software of "beagle2vcf.jar". Can I change it to plink *.ped (<0.5 is genotype of 0 and >1.5 is the genotype of 2) format first in R and convert it to the *.bed in plink? Any comments would be appreciated.
Thanks in advance
Ting
Created by Jian Yang jianyangqt The files as they are can be read into plink using the --import-dosage command, which fairly flexibly reads dosages from text files. You'll also need the .fam file contained in this folder, and I think optionally you can make a .map file by parsing the first 3 columns of the files, because the variants are labeled by the chromosome and location. See "PLINK 1 dosage" in the documentation: https://www.cog-genomics.org/plink/2.0/input.
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