How can you update vcf when one of the columns is CHR:POS:REF:ALT using bcftools?

Question

[kl]

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

[Mark]

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

[kl]

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

[Mark]

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