I'm trying to check the variations inserted by vcf-consensus in my new consensus fasta. I mean, I have a vcf file and the reference, and I have used vcf-consensus to produce a new fasta. I have a script that checks the length of the indels in my vcf, and the length of fasta files. So, I have assumed that:
length of my reference - deletions length + insertions length = new reference length
But the calculation gives me different results, and this is why I'm here. So, there is a way to check out which variations have been inserted by vcf-consensus? Maybe it performs some filter I don't know... My vcf only contains homozigous variations.
Thanks in advance