How can you update vcf when one of the columns is CHR:POS:REF:ALT using bcftools?
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4.3 years ago
kl ▴ 10

Hello,

How can you replace the column that is CHR:POS:REF:ALT as rsid name using BCFtools for a vcf v4.2 file?

Many thanks

bcftools • 1.4k views
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That's weird task to undertake. a VCF file should have an ID column which you can use to input the rsid.

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It does - the ID column is CHR:POS:REF:ALT.

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That's very strange! How was the vcf file made (i.e. how were variants called?). Also can you post an example (formatted correctly)?

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