Merge 2 imputation reference panels

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2.3 years ago

GiantSilverSoy ▴ 130

Hi,

Do you guys know if there is any other method to generate a merged imputation reference panel from 2 phased VCFs? There is the -merge-ref-panels function in the IMPUTE2 but I wonder if there is any newer or more updated method besides this, preferably with phased VCFs as input. Thanks!

panel Reference Imputation • 1.0k views

ADD COMMENT • link 2.3 years ago by GiantSilverSoy ▴ 130

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Not quite what you're asking for but this looks like it could be useful https://www.sciencedirect.com/science/article/pii/S0002929722001501

ADD REPLY • link 2.3 years ago by 4galaxy77 2.9k

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This is great. Not sure how MetaMinimac2 will go with imputed datasets from IMPUTE2 but it should be fine. Will try it. Thanks!

ADD REPLY • link 2.3 years ago by GiantSilverSoy ▴ 130

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I got no luck with MetaMinimac2 installation on the HPC, possibly because I can't use sudo. I have to look for a new way now.

ADD REPLY • link 2.3 years ago by GiantSilverSoy ▴ 130

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