Merging snp from different references into one vcf file

Question

[felipe-bita]

HI guys,

I'm here to ask your help in one thing that i have to do in my work, basically what i want to do is merge different VCFs files into one. This different VCFs are from different references used in the SNP calling, the specie that i study do not have a sequenced genome, so we are using genomes from close species. As you probably know, when i merge the VCFs i'm going to have a lot of "duplicated" markers with the same information. So, i'm looking for a approach to identify this markers and hold only one, i know i can write a script for this, but i would like know if you guys know any software that do this and how they compare the markers and conclude if they are or not duplicated.

I appreciate any help, Thanks Felipe Martins.

[felipe-bita]

HI, i'm very grateful for your help but i think it is not my problem. What i want to say is that despite the markers beeing found in different reference, they have the same information for all my samples. I want to find and remove this markers.

Answer 1

[Istvan Albert]

See this advice

bcftools merge of multiple vcf produces duplicate records. How to solve the issue.