How to Remove Phasing Information from a VCF File?

Can you just change pipe "|" to slash "/" in genotype GT field with e.g. bcftools annotate --set-format '%GT=[%TGT]\n'?

phasing

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updated 1.1 years ago by Mwangana •

• written 3.3 years ago by optimistsso4co3 •

1 answer

bcftools +setGT   in.vcf -- -t a -n u

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written 3.3 years ago by Pierre Lindenbaum

How can I use bcftools +setGT to get genotypes without phase e.g. "|" or "/"? For example, instead of 1|1 or 1/1, I would like to get 11

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written 1.1 years ago by Mwangana •

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