Question: Impute2 dosage file into standard Plink files
0
gravatar for rahapazoki
4.7 years ago by
rahapazoki10
European Union
rahapazoki10 wrote:

Hi all,

Anyone knows how to convert Impute2 dosage file to standard Plink files?

 

Thanks,

myposts • 2.4k views
ADD COMMENTlink modified 4.7 years ago • written 4.7 years ago by rahapazoki10
1
gravatar for rahapazoki
4.7 years ago by
rahapazoki10
European Union
rahapazoki10 wrote:

I heard that the gtool can help doing that. http://www.well.ox.ac.uk/~cfreeman/software/gwas/gtool.html

 

ADD COMMENTlink written 4.7 years ago by rahapazoki10
2

Yes, this command is generating a ped file

gtool -G --g example/example.gen --s example/example.sample

You can also specify --ped,--map,--phenotype,--sex and --threshold. Fo example adding  --threshold 0.9 will convert the largest genotype probability over the threshold to a ped file genotype. 

 

 

ADD REPLYlink modified 4.7 years ago • written 4.7 years ago by Jimbou730
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