Merge different vcf files

Question

[caique.manochio]

Hi, I have some vcf files in which some ref alleles are different for the same region. Can I merge all vcf files or do I have to standardize these ref alleles?

[Ram]

Normalize them first using vt normalize or bcftools norm - they need to be in left-aligned parsimonious representation before you can do an accurate merge if required.