Hello, I ran parsnp using a 17 whole genomes. I picked one of these genomes to use as a reference, but kept the sequence file in the directory still. After running parsnp I looked at the VCF output and it seems that there are SNPs being called when the reference sequence is mapped against itself. Does this make sense? It should be the exact same sequence mapped against each other, so why would there be SNPs?
Thank you!
Hello, I ran parsnp using a 17 whole genomes. I picked one of these genomes to use as a reference, but kept the sequence file in the directory still. After running parsnp I looked at the VCF output and it seems that there are SNPs being called when the reference sequence is mapped against itself. Does this make sense? It should be the exact same sequence mapped against each other, so why would there be SNPs?
Thank you!