Question

How to Remove Phasing Information from a VCF File?

0

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2.2 years ago

optimistsso4co3 ▴ 140

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

phasing • 1.5k views

ADD COMMENT • link updated 2.2 years ago by Pierre Lindenbaum 166k • written 2.2 years ago by optimistsso4co3 ▴ 140

score 2 · Accepted Answer · 2023-05-06

2

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2.2 years ago

Pierre Lindenbaum 166k

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

ADD COMMENT • link 2.2 years ago by Pierre Lindenbaum 166k