Using PLINK for (ROH) analysis using full genome

Question

[taimur.al-said]

Hi,

I'm trying to create Binary PED files (.map, .fa. and .bim) or .map files to start running my ROH analysis.

plink --vcf *file.vcf* --make-bed --keep-allele-order --double-id --allow-extra-chr --out *out_plink*

The error it gives me when i convert my VCF to PED files is: variant records had no GT field. Error: PLINK does not support more than 2^31 - 3 variants. We recommend other software, such as PLINK/SEQ, for very deep studies of small numbers of genomes.

Can someone please advice what to do?

Regards, Taimur