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.