Dear bioinformaticians,

A few months ago I started to analyze Mutation Accumulation Lines (MAL) for single nucleotide polymorphism. It was my first time and I had to create a VCF file for the new reference genome and it took a lot of time and finally I figured it out. With the data, we are comparing the mutation accumulations from the F0 to F5. For the F0, I had two different genomes, POOL and POOL1. I though they are different, but today, I have been told that they are the same sample that sequenced 2 times. But I already created the VCF file and used that file to recalibrate the BAM files.

What I am asking that, is it okay to create the VCF file with the 2 sequences that belongs to the same sample or should I concatenate them and start all over again?