Question

missing REF and ALT in vcf

0

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2.8 years ago

raalsuwaidi ▴ 100

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?

REF SNP VCF ALT • 1.0k views

ADD COMMENT • link 2.8 years ago by raalsuwaidi ▴ 100

Ram · Answer 1 · 2021-06-28

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2.8 years ago

Pierre Lindenbaum 161k

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

ADD COMMENT • link updated 2.8 years ago by Ram 43k • written 2.8 years ago by Pierre Lindenbaum 161k

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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?

ADD REPLY • link 2.8 years ago by raalsuwaidi ▴ 100