Bcftools equivalent of vcftools conversion to ped & map

Question

[dec986]

I am converting a VCF to ped & map thus in vcftools

vcftools --gzvcf ZZZZZTYT.vcf.gz --plink --out ZZZZZTYT

which works fine.

However, I have been searching and searching, can bcftools do the same with a bcf?

Answer 1

[chrchang523]

You should unlearn this vcftools command.

1. The .ped + .map format has been obsolete for close to a decade. The plink .bed+.bim+.fam binary format is simultaneously much more efficient and able to store more information (minor alleles not present in the immediate dataset are not lost). Or if you want to keep your data as human-readable text, just keep using VCF; plink has had much better support for VCF than .ped + .map since 2017.
2. Even when there is a legitimate reason to convert to .ped + .map (e.g. to use a 15-year-old script), you are better off using plink2 --vcf ... --export ped or plink2 --bcf ... --export ped for this conversion.