conversion of VCF to M3VCF using Minimac
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Entering edit mode
21 months ago
dec986 ▴ 330

I'm attempting to convert a VCF into a M3VCF.

I've been looking at https://genome.sph.umich.edu/wiki/M3VCF_Files and https://genome.sph.umich.edu/wiki/Minimac3 and supposedly minimac3 can convert, but the exact command line syntax is a mystery.

I've tried Minimac3 --refHaps chrX.F.vcf.gz --processReference --prefix tmp

but this says that Missing Value for Individual : ZBAZDCC at Marker : X:167699 but there's nothing that I can do about this, this is a sample failure.

Using minimac4 --refHaps chrX.F.vcf.gz --haps chrX.F.vcf.gz --processReference --prefix tmp --ignoreDuplicates I get another error:

ERROR !!! 
 VCF Format detected ...
 The current version of Minimac4 can ONLY handle M3VCF files for imputation 
 Please convert the VCF file to M3VCF using Minimac3 
 We will implement this feature in Minimac4 very soon

so the most recent version (minimac4) can't do this at all, I have to use the older minimac3.

How can I convert VCF to M3VCF?

minimac • 1.1k views
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Entering edit mode
19 months ago
awakumaya ▴ 20

You should do gunzip the chrX.F.vcf.gz. I could solve it by giving the gunzipped vcf file to minimac3.

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