How can I make plink binary files (bed, bim, fam) for Ag1000G SNP data?

[alimanfoo]

Some programs such as EEMS need plink binary format files for input. Ag1000G only releases SNP data in VCF and Zarr formats. What's the best way to generate plink files?

[alimanfoo]

Converting from VCF is currently the only option, as far as I'm aware. I haven't tried it myself, but it looks like plink can do it, e.g.:

$ plink --vcf <vcf_file> --make-bed --out <output_fileset>

Note that binary plink can only support biallelic variants as far as I'm aware. So for Ag1000G phase 2 you'd want to start from the prefiltered biallelic VCFs, available at:

• ftp://ngs.sanger.ac.uk/production/ag1000g/phase2/AR1/variation/main/vcf/biallelic/

For Ag1000G phase 3 SNP data, some more work is needed to merge VCFs for the samples of interest then select biallelic SNPs only. Some more info on handlinge phase 3 SNP VCFs is here.

P.S., It would be nice to have a zarr to plink converter as it would probably be lot faster than going from VCF, something to add to the wish list.