How does Minimac4 handle large chunks of missing genotype when creating reference panel

[JoannaTan]

Hi,

I am trying to impute my data using my own reference panel.

However, my reference panel has many blocks of missing genotypes.

I am wondering if minimac4 can handle a reference panel with large blocks of missing genotype information and what are the problems that may occur during the generation of M3VCF if the reference panel has large blocks of missing genotypes.

Please advice.

Thank you.

Best regards, Joanna

[thheng]

I am curious about this too, thank you!

[jonathonl]

The reference panel should be phased and most phasing software will impute missing genotypes while phasing.

[jonathonl]

Note: Minimac4 expects the reference panel to be sourced from whole genome sequence date.

[thheng]

thank you