BOLT-LMM/BGEN/phase-data

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Matthew Maher

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Apr 30, 2022, 12:21:40 PM4/30/22
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Hi!

I have what I believe is a followup question to this earlier thread about PLINK2/BOLT-LMM and BGEN-1.2 format:  https://groups.google.com/g/plink2-users/c/BxdcU5Cmvow/m/HluKjCtIBwAJ

BOLT-LMM sadly does not seem to support dosages in PGEN format, and so its documentation recommends using "plink2 --export bgen-1.2 bits=8" to create BGENs.    When I do that I encounter the same error as in that earlier thread ("ERROR: <var> has Phased = 2 (not 0)").  In that earlier thread, Christopher responded:

"BOLT-LMM does not support bgen-1.2 phased dosages, so you need to remove phase information before exporting to bgen-1.2"

and he supplies commands for dropping the phase information on the import from VCF.

But in my case, I only have the PGENs.  Do I need to round-trip the data to VCF and back in order to lose the phase information or is there some other option (to --make-pgen perhaps) that does that?  I looked and I'm not seeing any such option, but maybe I'm missing it. 

Secondarily, I'm puzzled by the detail of that error message that seems to indicate PLINK2 created BGEN files with "Phased = 2", while the BGEN 1.2 spec seems to say that only 0 or 1 are valid values for 'Phased'.   Is perhaps the error message simply wrong (that's a BOLT question, I guess), or perhaps the spec has been extended and '2' is defined?  

Thanks for any info and thanks for PLINK(2)!

Christopher Chang

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Apr 30, 2022, 2:52:13 PM4/30/22
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--make-pgen's "erase-phase" modifier is what you're looking for.

Matthew Maher

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Apr 30, 2022, 5:49:04 PM4/30/22
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thanks.  And now I'll go schedule an eye exam, as I have no idea how I didn't see that. 
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