Remove duplicate lines in a vcf file

Question

[Patrick]

I have a vcf file that I created from 23andme raw data results.

In this vcf file, there are lines that have the exact same chromosome number and position, however they have a different rsID. Here is a screenshot:

They are causing errors in a program I am trying to run for PRS calculation. Should I remove them and how can I do that? If I remove them, which one do I keep?

I searched for similar questions online, but couldn't find anything that resembles my exact situation.

[Pierre Lindenbaum]

you got answers to your previous questions, please mark them as answered if needed Where can I find a vcf file with individuals in it, that have a specific disease? ; Can I remove all variants in a vcf file that have 0/0 for PRS calculation? ; How to convert a 23andme.txt file to a vcf file? ; ...

[Patrick]

Sry I forgot to mark them.

Answer 1

[Pierre Lindenbaum]

bcftools norm --remove-duplicates

If I remove them, which one do I keep?

you just have a different ID, so you don't really care...