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genetica:impute

Imputation with impute2

Very basic use:
  • -g <input file> - database to input (see format below)
  • -m <map> - recombination map as 1000Genome or something like this
  • -int <lower> <upper> - interval to make the imputation
Input file format

First convert the binary files to .ped and .map if needed

http://pngu.mgh.harvard.edu/~purcell/plink/dataman.shtml

then you can use gtool,

http://www.well.ox.ac.uk/~cfreeman/software/gwas/gtool.html

in particular, http://www.well.ox.ac.uk/~cfreeman/software/gwas/gtool.html#PED to GEN Conversion

gtool -P --ped example/example.ped --map example/example.map --og example/out.gen --os example/out.sample

Before this some awkward work need to be done

Look an example here

genetica/impute.txt · Last modified: 2020/08/04 10:58 (external edit)