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Impute2 dosage file into standard Plink files

Hi all,

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

Thanks

plink impute2
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updated by Ram Ram • written by rahapazoki • rahapazoki

2 answers

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. For example adding --threshold 0.9 will convert the largest genotype probability over the threshold to a ped file genotype.

• 0 views • link
updated by Ram Ram • written by Jimbou Jimbou

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

• 0 views • link
updated by Ram Ram • written by rahapazoki • rahapazoki

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