missing REF and ALT in vcf

Question

[raalsuwaidi]

is there a tool or a way where i can select some SNPs and have the values for the REF and ALT set to missing (replaced by ".") or do i have to do pure coding?

Answer 1

[Pierre Lindenbaum]

bcftools view --uncalled in.vcf
bcftools view -i 'COUNT(GT="mis")>0'  in.vcf

[raalsuwaidi]

Thank you for such a fast response.

But I actually want to change the genotype values to be missing so I can run it through imputation. Will you be able to help?