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