ANNOVAR annotates delition and duplications with different co-ordinates

Question

[Manuel]

I am comparing SNPEFF, VEP and ANNOVAR against manually curated annotation done by the clinical genetics team I am working with. I am doing this for training porpoise. This is the results I have got

My question is why ANNOVAR annotates del, ins and dup with slightly differences in the co-ordinates. Is this because this is wrong or because I am missing something?