I'm trying to merge two VCF files, but I'm running into an error message that says The REF prefixes differ: G vs A (1,1) Failed to merge alleles at 1:88143 in sheep2_50KOAR3.1_student_project.vcf.gz. I'm not sure how to fix this error. Can someone help me understand what is causing this error and how to resolve it?

Here is the command I used to merge the files:

bcftools merge sheep1_50KOAR3.1_student_project.vcf sheep2_50KOAR3.1_student_project.vcf -Ov -o sheepcombined_50KOAR3.1_student_project.vcf

Both files have SNP data from the Illumina 50k Ovine SNP, and I believe were generated using the same reference genome. I'm not sure what could be causing this error. Any help would be greatly appreciated.

Thank you!

  • $\begingroup$ We can't help you handle data we cannot see. Please edit your question and add the two files. We need i) the full headers from both files and ii) the variant(s) that cause the error. Presumably, you have a variant at position 88143 of chr1 that is causing this error. $\endgroup$
    – terdon
    Commented Apr 1, 2023 at 14:22


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