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Santy-8128 / Minimac3

Minimac3 is a low memory and computationally efficient implementation of the genotype imputation algorithms. Minimac3 is designed to handle very large reference panels in a more computationally efficient way with no loss of accuracy.
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reference panel with missing genotypes #12

Open mfz opened 4 years ago

mfz commented 4 years ago

Good day!

Thank you for making Minimac available!

I am trying to convert a reference panel to M3VCF format using

Minimac3 --refHaps refpanel.vcf.gz --processReference --prefix ReferencePanel

but I get an error message "Missing Value for Individual: xxx at Marker: xxxxx"

Looking at the vcf file, the genotype in question is '.|0'

Is there any way to allow missing genotypes? Or can Minimac directly impute them?

If I use a small version of the VCF file with only a few markers the program finishes successfully.

The version of minimac I am using is f142810

Best regards, Florian

Santy-8128 commented 4 years ago

m3vcf file is for the reference panel. The reference panel cannot have any missing values, hence you are getting the error.

Regards, Sayantan Das,

23andMe

On Tue, Nov 12, 2019 at 12:34 AM mfz notifications@github.com wrote:

Good day!

Thank you for making Minimac available!

I am trying to convert a reference panel to M3VCF format using

Minimac3 --refHaps refpanel.vcf.gz --processReference --prefix ReferencePanel

but I get an error message "Missing Value for Individual: xxx at Marker: xxxxx"

Looking at the vcf file, the genotype in question is '.|0'

Is there any way to allow missing genotypes? Or can Minimac directly impute them?

If I use a small version of the VCF file with only a few markers the program finishes successfully.

The version of minimac I am using is f142810 https://github.com/Santy-8128/Minimac3/commit/f14281027e9b1686e22f50501d2f7751e47724d9

Best regards, Florian

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