plinkfile and bgen file with dosage

saigegit / SAIGE

Development for SAIGE and SAIGE-GENE(+)

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plinkfile and bgen file with dosage #36

Closed xingejun closed 2 years ago

xingejun commented 2 years ago

Hi Wei,

I am confused with if SAIGE and SAIGE-GENE support the dosage(DS) imputed not GT for input of plinkfile or bgen file and how to set the parameter to do it.

Looking forward to your reply! Xinxin

saigegit commented 2 years ago

Hi Xinxin,

SAIGE and SAIGE-GENE support the bgen (contains dosages) and plink binary file (bim, bed, fam contains genotypes). For VCF, both are DS and GT are supported with --vcfField=GT or DS specified.

Thanks, Wei

xingejun commented 2 years ago

Hi Wei,

Thanks for your reply!

Xinxin