I assembled a viral genome using two different assemblers e.g., Megahit and Metaspades. Both the assemblers uses de bruijn graphs but might use different k-mers because both the assemblers uses multi k-mer approach to find optimum k-mer.
I aligned the contigs to the reference and called variants using BCFtools. I am getting 18 SNPs that are found in one of the assemblers. Im surprised to see the degree of disagreement in variant calling between two assembly methods. Is it expected or what would be the possible explanation for that?