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