Question: is it .impute2 format equal to .gen format
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Peter Chung • 120 wrote:
I would like to apply qctool software from .impute2 format to .bgen format. However,
qctool -g HELLO.impute2 -og HELLO.bgen
Error comes out:
!! Error (genfile::BadArgumentError): In argument(s) filetype_hint="guess", inferred type = "" to function genfile::SNPDataSource::create(): Unrecognised file type..
So I should transform the .impute2 format to .gen format then to .bgen format.
But I checked on the file that the format of impute2 is same as gen format.
So anyone know how to apply the qctool package to the .impute2 file
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modified 8 months ago
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Kevin Blighe ♦ 63k
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written
3.1 years ago by
Peter Chung • 120
IMPUTE2 should produce output in GEN format. How have you run IMPUTE?, i.e., how was
HELLO.impute2produced?