[feature request] Add support for VCF files about admixtools HOT 3 CLOSED

The admixtools methods don't use any information that is in VCF files but not in plink files. So even if you wouldn't explicitly convert VCF to plink, any information other than the 0/1/2 genotype calls would be discarded anyway if admixtools read VCFs directly. Allele polarization also doesn't matter for admixtools.
If you have VCF files and don't want to use any of that extra information to filter SNPs or genotypes, then you can just use plink or something similar to do the conversion.
If you do want to use that extra information in some way, then that's a task which is outside the scope of what admixtools does.

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No worries, glad you like it!

I'm not sure which issues you are thinking of in going from VCF to plink or eigenstrat formats, but I assume they have to do with the fact that there is not an unambiguous way to convert VCF to plink, with many edge cases that could be handled in several different ways. I doubt that I could implement this conversion any better than existing programs. So I think the best solution would be to use plink or a similar program to convert VCF to plink.

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Hi Robert,

Many thanks for your quick response. There are a number of issues associated with the conversation from VCF to plink and vice-versa. First of all, there's a huge information loss of all non-genotype data that the user might want to come back to. Also, there are a number of documented issues related to allele polarisation in plink, and datasets merging to list a few.

To read in a vcf, external libraries such as vcfR or PopGenome can be used.

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