How to remove duplicate SNP IDs from VCF files?

Question

[anikcropscience]

Hello, I have a VCF file containing ~900K SNPs. There are some tri-allelic SNPs in the dataset. So, I used bcftools to split those tri-allelic SNPs into biallelic SNPs. Then I tried to remove the duplicated SNP IDs that were generated after splitting the tri-allelic SNPs. I used bcftools as well but the code is not removing the Duplicated SNP IDs. I used the following command for splitting the tri-allelic SNPs:

bcftools norm -m-any --output output.vcf input.vcf

And for removing the duplicate SNPs, I used the following code:

bcftools norm --remove-duplicates --output output.vcf input.vcf

Can anyone please suggest to resolve this issue?

[brunobsouzaa]

I believe you have to tell bcftools to remove snps inside the argument. Can you plz try this: bcftools norm --rm-dup snps --output output.vcf input.vcf Just made a test here and it worked. I'm using bcftools V 1.10.2

[anikcropscience]

I have tried this withs snps/all. But still showing the same output.

Answer 1

[Kevin Blighe]

You can handle these in different ways:

• A: Remove duplicate SNPs only based on SNP ID in bcftools

Kevin

[anikcropscience]

I saw this post and used the --remove-duplicates command. But it is not working at all.