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Combine 2 VCF with different references

d_nid_ni Posts: 17Member


So today I have to compare two different vcf (from different pipelines, only one of them is from GATK) and when I tried to combine it with combineVariants, I had an error because the references doesn't match:

The provided variant file(s) have inconsistent references for the same position(s) at chr1:1724719, A* vs. G*

I know why it's happening, but I don't know if there is an option/tools to "fix" the vcf from the other pipeline.

That I want to do is take the VCF created with a "bad" reference and use a command or GATK option to "fix" it according with the correct reference fasta file.

Thanks for your help!


Best Answer


  • d_nid_ni Posts: 17Member

    It doesn't solve my problem, because I don't know which is the original reference... but maybe useful for other.


  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 10,469Administrator, Dev admin

    Have you checked the VCF header? Depending on the tool that created it it might contain reference information.

    Geraldine Van der Auwera, PhD

  • d_nid_ni Posts: 17Member

    Hi Geraldine,

    I created this vcf by myself with custom scripts from microarray data, so finally, I changed my code to check the reference (the same as I use for GATK) and now it's working fine.


  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 10,469Administrator, Dev admin

    Great, always glad to hear when a problem goes away :)

    Geraldine Van der Auwera, PhD

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